In early summer, Judy and Dennis Shepard bought airline tickets to give a speech to the workforce at CIA headquarters in Langley, Virginia. The Shepards in 1998 had founded the Matthew Shepard Foundation in honour of their late son — a 21-year-old college freshman who was viciously attacked and left tied to a fence before he was brought to a hospital where he died of his injuries.

One of the most notorious anti-gay acts of violence in American history, his death led to some of the country’s first federal hate-crime laws.

The Shepards had been invited to the CIA to talk about diversity and LGBTQ rights, joining a long line of guest speakers at the covert overseas spy agency, including lawmakers, former officials, authors and celebrities.

The schedule was set, and the details arranged, but in the eleventh hour, the senior leadership shut down the event. The seventh floor, where the director’s office sits, had the Shepards’ speech cancelled, questioning what value it would bring to the CIA mission.

Three sources described the events, requesting anonymity to speak freely about internal agency matters.

It took several weeks for the family to be reimbursed for their travel, one source told Foreign Policy. The Shepard Foundation did not respond to a request for comment.

The cancellation, now under review by the CIA’s Office of General Counsel, according to a second source, left employees disheartened — particularly those invested in the diversity reforms that were emphasised during the tenure of John Brennan, the former CIA director.

The CIA described the reasons for the cancellation as “materially false”, but confirmed the event had been scheduled. “As we explained to the Shepards, CIA decided on a Pride month event with a national security focus and the event with Senator [Tammy] Baldwin achieved that goal,” an agency spokesman told Foreign Policy.

For those who have worked inside the agency, the backtracking on diversity represents a threat to the workforce and national security, according to Nada Bakos, a former CIA analyst who helped to track high-level terrorist targets such as Abu Musab al-Zarqawi.

The agency needs employees from different backgrounds and orientations to effectively recruit agents abroad. “What if you have to recruit someone who’s gay and that’s the only reason they’re talking to you?” she asked.

“This isn’t just about today’s diversity issue. It’s about tomorrow’s lack of diversity that will erode the agency,” Bakos told Foreign Policy. “You can’t hire someone who’s typically white American to walk around Baghdad.”

Until the 1990s, being openly gay or transgender was a career-ending taboo kept secret among officers. The agency was fearful that employees’ personal relationships would serve as valuable blackmail for adversaries overseas. Exposure would likely result in the loss of security clearances, rendering analysts and officers unemployable in the field of intelligence.

The situation for women and minorities was little better, particularly when it came to high-profile assignments such as production of the President’s daily brief, a summary of top-secret intelligence given to the President every morning. “The most important intelligence product ... during the 1950s and 1960s and 1970s was essentially produced by old white men,” said David Priess, a former CIA briefer and author of The President’s Book of Secrets.

In 1995, President Bill Clinton issued an executive order that prevented intelligence officers from losing their clearances on the basis of their sexuality, kicking off what was to be a long and hard-fought shift in agency culture.

In March 2013, John Brennan was appointed director under President Barack Obama, and the new CIA head moved to make diversity and employee rights a priority. Senior leaders competed for spots to speak at employee gay pride events and accompanied the director to diversity events and celebrations.

While embraced by many, Brennan’s policies drew the ire of right-wing publications such as the National Review, which claimed his diversity and inclusion strategy was just a way to make the agency more “politically correct”.

But for Brennan, the changes were a matter of building a better workforce, as well as national security. “I believe strongly that diversity and inclusion [are] what this country is all about,” Brennan said in a phone interview with Foreign Policy. “I can think of no organisation that can make a better business case for diversity and inclusion than the CIA. We have the responsibility of covering the globe, understanding all societies, cultures, and backgrounds.”

Brennan left the CIA in January, on Obama’s last day in office. As he was on his way out the door, he left an action plan and a team of workers to continue implementing diversity and inclusion efforts that he had begun while director, he said.

“The team implementing the CIA’s efforts to build a diverse workforce, which is led by a senior agency officer fully dedicated to this task, is still in place and working on these efforts,” the CIA spokesman said. “See our website, which continues to publish that strategy. Having said that, Director [Mike] Pompeo has now seen the data and believes that previous efforts have failed to sufficiently increase the diversity of our recruitment pipeline.”

Things changed quickly with President Donald Trump’s pick for CIA director, Mike Pompeo. A West Point graduate and former small-business owner, he never made a secret of his conservative social viewpoints during his time as a lawmaker. He has visited college campuses to talk about his disapproval of same-sex marriage, arguing that “the strength of these families having a father and a mother is the ideal condition for childbearing.”

He has sponsored several pieces of legislation that would have weakened the rights of gay couples and supported organisations that champion those same beliefs.

Kamala Harris, a Democratic senator from California, pressed Pompeo during his confirmation hearing on whether he would support the rights of his LGBTQ employees. He promised that he would treat all his employees in a way that is “appropriate and equal”.

But when he entered the building in late January, the former Republican lawmaker from Kansas publicly and privately snubbed calls for his commitment to diversity, according to multiple sources.

In June, the intelligence community held its pride summit at FBI headquarters. Speakers included Andrew McCabe, then the acting FBI Director, who said the intelligence community’s credibility derived from the importance it placed on diversity. “We all need to be allies, to walk in each other’s shoes, to try to understand what it’s like, for example, to be gay, a person of colour, or transgender, or all of these at the same time,” he said in a keynote speech. Pompeo did not attend the summit. Dan Coats, the director of national intelligence, did not attend, either, but he sent prepared remarks to the workforce beforehand expressing his commitment to hiring from the “widest pool of talent” possible and protecting his employees from discrimination. Coats’s acting deputy, Dawn Eilenberger, appeared in his stead.

“Several senior CIA leaders and many other CIA officers attended and participated in this event, just as they have in past years,” the CIA spokesman said, but did not offer a reason why Pompeo did not attend.

Questions about his commitment to diversity continued to dog Pompeo, however.

During his very first all-hands speech to the CIA workforce, Pompeo cheered the officers and analysts, pledging to support them. But on the issue of diversity, Pompeo’s response raised concerns. According to two sources familiar with the speech, he was repeatedly asked about his commitment to diversity. After the third question, he visibly lost his temper. He snapped back, saying he did not know what people wanted him to do besides seek out the best person for the job, one source who was present at the speech recalled.

“He didn’t seem to understand the need for a workforce that reflects America,” another source familiar with speech noted.

The CIA disputed this characterisation. “Director Pompeo has consistently, repeatedly and unrelentingly expressed his commitment to hiring the best person to perform each and every national security mission at CIA, wherever we can find them,” the spokesman said. “There is zero room for discrimination of any kind and it will not be tolerated by anyone on our team.”

At the Aspen Security Forum in Colorado in late July, Pompeo responded to a question about his dedication to hiring for diversity, specifically for women. He said only that he always wants the “best person” for the job regardless of their gender.

During his first eight months at the CIA, Pompeo has expressed little interest in attending diversity-related events, including those designed to honour the work of those at the agency, and also to recruit from minority communities at universities and other locations. One source familiar with the matter noted that Pompeo stated he should be called upon to attend a diversity event only as a last resort and preferred other senior leaders to go in his place.

When asked if Pompeo had attended any diversity events, the spokesman instead referred to Pompeo’s commitment to hiring the best person.

“Whether that person is an African-American IT professional from New York, a Pashtun-speaking Italian from Montana or a Hmong scholar from Mississippi, there is only one question: can that person deliver the mission they are tasked with undertaking to keep America safe?” the spokesman said.

“This is heartbreaking,” said Bakos, the former CIA analyst, of reports that diversity efforts are backsliding. “It’s already too easy to get these flag-waving, chest-bumping people” hired into the agency.

Some recently retired intelligence officers worry that Pompeo’s approach could mean the agency is headed in a damaging direction.

“An intelligence service that purposefully excludes and marginalises people is making the conscious decision to limit the success of their service and their country,” one former intelligence official who served under Brennan wrote in a message to Foreign Policy.

Brennan, the former CIA director who is now a fellow at the Fordham University School of Law, declined to comment on any of his successor’s decisions, but told Foreign Policy that he met with the workforce before his departure on several occasions and communicated to them that the agency’s progress on diversity and inclusion over the years had been significant, but that it was up to them to keep it moving forward.

“It’s up to you to make sure it’s not going to be reversible,” he recalled telling them. “If [you] see something that is wrong or not in keeping with the agency’s commitment to diversity and inclusion, [you] need to speak up and speak out.’”

Brennan was particularly concerned about the alienation of the CIA’s Muslim employees. “Over the last couple years, we really tried to make a real effort to have the Muslims within the CIA workforce feel that they were as special and as valued and important as everyone else,” Brennan said. “Too often, there has been unfortunate rhetoric that has been the equivalent of Muslim bashing. A lot of employees took that rather personally.”

Pompeo, an evangelical Christian, has said previously that Islamist terrorists will “continue to press against us until we make sure that we pray and stand and fight and make sure that we know that Jesus Christ our saviour is truly the only solution for our world.”

The concerns are not that Pompeo is religious, but that his religious convictions are bleeding over into the CIA.

According to four sources familiar with the matter, Pompeo, who attends weekly Bible studies held in government buildings, referenced God and Christianity repeatedly in his first all-hands speech and in a recent trip report while travelling overseas. According to a profile by The Washington Post’s Greg Miller, Pompeo is working on starting a chaplaincy for the CIA campus like the military has.

The CIA did not dispute these events. “Director Pompeo is a man of faith,” the spokesman said. “The idea that he should not practise his faith because he is Director of CIA is absurd.”

Michael Weinstein, a former Air Force officer who founded the Military Religious Freedom Foundation, says he has been seeing increasing complaints from those inside the intelligence community. Weinstein’s foundation, which focuses on preventing religious pressure from creeping into the military, also has clients in the intelligence community, mostly from the CIA, the National Security Agency, and the Defence Intelligence Agency.

According to Weinstein, agency employees do not want to go public with their complaints because of fear of retribution or being labelled as “leakers”. They do not typically file formal complaints within the Government. But certain things are making them especially uncomfortable, such as officials signing off with the phrase “have a blessed day”.

That is something “straight out of The Handmaid’s Tale, Weinstein said.

The spokesman added: “We are unaware of any such complaints being registered at CIA.”

The foundation’s intelligence-community clients have doubled since the July 2016 Republican National Convention, Weinstein said. While he would not specify the number of intelligence-community clients he works with, Weinstein said it was in the hundreds — the majority of them working out of Langley. “In the intelligence community, we see supervisors wanting to hold Bible studies during duty hours [and] inviting lower-ranking individuals to their homes for Bible studies,” Weinstein told Foreign Policy.

Whether it is pressure to attend Bible study or concerns that the annual holiday party will become a Christmas party, agency employees feel on edge, according to Weinstein. “Our clients at CIA feel extremely isolated in a way they have not felt before,” he said.

The CIA insists that “Pompeo and his senior leaders” have their own view of diversity. “They demonstrate their commitment to the diversity required to achieve that mission in the most important way possible: by living the creed of crushing our adversaries by hiring and training the best spies the world will ever know.”

• Jenna McLaughlin is an intelligence reporter for Foreign Policy, focusing on the culture, dynamics and events happening in the National Security Agency, the Central Intelligence Agency and the other 15 members of the intelligence community — plus the way the sensitive information they gather and analyse informs and directs the White House and policymakers on the Hill