When Raegan Zelaya and Shua Wilmot decided to include their pronouns at the end of their work emails, they thought they were doing a good thing: following what they viewed as an emerging professional standard, and also sending a message of inclusivity at the Christian university where they worked.

But their bosses at Houghton University, in upstate New York, saw the matter very differently.

Administrators at Houghton, which is affiliated with a conservative branch of the Methodist Church, asked Ms. Zelaya and Mr. Wilmot, two residence hall directors, to remove the words “she/her” and “he/him” from their email signatures, saying they violated a new policy. When they refused to do so, both employees were fired, just weeks before the end of the semester.

Houghton’s firing of the two staff members has dismayed some of its alumni, nearly 600 of whom signed a petition in protest. And it comes as gender and sexuality have become major fault lines in an increasingly divided nation, and after other faith-based organizations, including Yeshiva University in Manhattan, have argued that First Amendment protections of religious freedom allow them to treat gay and transgender people differently than others.

As Republican lawmakers across the country have sought to energize their base by passing laws restricting gender-transition health care and banning drag performances and classroom instruction about sexual orientation and gender identity, Christian colleges have become staging grounds in these escalating debates.

In particular, institutions like Hillsdale College in Michigan and Liberty University in Virginia have taken central roles, both producing and attracting leaders of the movement.

With fewer than 1,000 students, Houghton is smaller and off the beaten track, but it has made other recent moves that put it in line with its conservative Christian peers, and that have alarmed some alumni. Since 2021, it has closed a multicultural student center and an environmental sustainability program and rescinded its recognition of an on-campus L.G.B.T.Q. club after the club declined to more promote conservative views on sex and gender.

“I think it boils down to: They want to be trans-exclusive and they want to communicate that to potential students and the parents of potential students,” Mr. Wilmot said of his firing.

Ms. Zelaya and Mr. Wilmot, neither of whom is transgender, said they had professional and pastoral reasons for including their pronouns, but also a practical one: They both have uncommon, gender-neutral names, and said they have often been misgendered in email correspondence.

“There’s the professional piece to it, and the practical piece, and there’s also an inclusive piece, and I think that’s the piece this institution doesn’t want,” Mr. Wilmot, 29, said.

Michael Blankenship, a university spokesman, said in a statement that Houghton “has never terminated an employment relationship based solely on the use of pronouns in staff email signatures.”

“Over the past years, we’ve required anything extraneous be removed from email signatures, including Scripture quotes,” he said.

In Ms. Zelaya’s termination letter, a photo of which was widely shared online, she was told she was fired “as a result of your refusal to remove pronouns in your email signature” as well as for criticizing an administration decision to the student newspaper.

Houghton University is affiliated with the Wesleyan Church, which teaches that “gender confusion and dysphoria are ultimately the biological, psychological, social and spiritual consequences of the human race’s fallen condition.” It views “adult gender nonconformity as a violation of the sanctity of human life.”

The university maintains a public declaration of its beliefs, describing itself as “solidly Biblical” and saying the teachings of the Wesleyan Church are “central everywhere” on campus.

“Sometimes, this means affirming positions currently called conservative,” Houghton’s statement of belief says. “For example, we privilege the understanding of marriage as between a man and a woman, and the sanctity of life from conception to natural death.”

But Houghton’s statement of belief also expresses some positions that conservatives might disagree with, including an acceptance of women into the priesthood and the belief “that we have significant work to do in healing the scars of racism in America.”

Some alumni said open debate and respect for differing views was what they valued about their time at Houghton. Almost 600 signed an open letter at the end of April protesting the termination of Ms. Zelaya and Mr. Wilmot, as well as other recent university decisions.

“Our overall concern is that these recent changes demonstrate a concerning pattern of failure on the part of the current administration to respect that faithful and active Christians reasonably hold a range of theological and ethical views,” the letter said.

Earlier this month, the university president, Wayne D. Lewis Jr., replied to the alumni letter. He said many of the decisions it mentioned, including the closure of the multicultural center and the sustainability program, had been budgetary moves meant to combat financial challenges brought about by “many years of enrollment and revenue decline and a significant structural budget deficit.”

And while he did not address the firing of Ms. Zelaya and Mr. Wilmot, he did reaffirm the university’s commitment to the teachings of the Wesleyan Church.

“Houghton unapologetically privileges an orthodox Christian worldview, rooted in the Wesleyan theological tradition,” the president wrote. He also noted that university employees were required to reaffirm their “understanding of and agreement to these commitments” at the start of each year.

Molly Connolly, 21, a sophomore and student council member who aspires to become a Wesleyan minister, said the administration’s decisions had caused “a lot of frustration” for students, who she said hold a wide range of political and religious beliefs. She helped organize a prayer vigil and a sit-in where students could voice their concerns, she said.

“People felt it was political and did not align with some people’s interpretation of what it means to be Christlike,” Ms. Connolly said. “This just highlighted how divided people are about politics and identity politics and how people understand gender and sexuality.”

Derek Schwabe, 33, a gay man who graduated from Houghton in 2012, said the campus “was never an affirming place” during his time there. He did not come out until after graduation, and said gay students mostly felt like “if you kept your head down you could survive.”

Nevertheless, Mr. Schwabe thought the administration at the time had taken a more neutral approach toward L.G.B.T.Q. issues, for example by allowing on-campus debates and other activities. For students from conservative families, like himself, those events could be revelatory.

“At the Houghton I knew, there was room for discussion and allowing differences of opinion,” Mr. Schwabe said. “I was exposed to broader viewpoints on these issues than I had been exposed to before. I am sad to see even that level of openness has been curtailed.”

In interviews, Ms. Zelaya and Mr. Wilmot said they believed their dispute with the school boiled down to a difference of opinion over how best to live a Christian life.

They included their pronouns because they wanted to engage with society’s downtrodden as Jesus Christ might have done, they said.

“At the end of the day, it has no bearing on what I actually believe or what I think is a sin or not a sin,” Ms. Zelaya, 27, said. “It all comes down to: Am I loving people in a way that reflects Christ?”

She said she thought their firings were instead motivated by the university’s decision to “toe the party line” and appeal to the conservative political beliefs that dominate the evangelical Christian world.

“We live in a very divided world right now where everything is this or that, right or left, conservative or liberal, Republican or Democrat,” Ms. Zelaya added. “As Christians, I think we’ve gotten so caught up in these ideas of, ‘This is what I should be advocating for or upset about,’ that we forget to actually care for people.”