The LDS-owned school will not rehire Nielsen after spring term because of his remarks in an op-ed piece earlier this month.
"I believe opposing gay marriage and seeking a constitutional amendment against it is immoral," the part-time philosophy teacher and practicing Latter-day Saint wrote in the June 4 Salt Lake Tribune.
Four days after the column ran, BYU Department of Philosophy Chairman Daniel Graham sent Nielsen a letter informing him of his dismissal.
"In accordance with the order of the church, we do not consider it our responsibility to correct, contradict or dismiss official pronouncements of the church," the letter reads. "Since you have chosen to contradict and oppose the church in an area of great concern to church leaders, and to do so in a public forum, we will not rehire you after the current term is over."
Besides losing his BYU job, Nielsen now fears he could lose something more precious: his church membership.
"I have no desire to be anything but a member," he said Tuesday in an interview.
LDS Church spokesman Mark Tuttle said members are free to voice their own opinions. He cited Senate Minority Leader Harry Reid, a Mormon who also opposes amending the Constitution to bar same-sex marriage.
The Nevada Democrat did, however, vote for a state constitutional amendment against same-sex marriage and also for the federal Defense of Marriage Act.
The problem for Nielsen is that he could not continue to collect a BYU paycheck while challenging church leaders.
Nielsen, who has taught at BYU for several years, said he was scheduled to teach classes summer, fall and winter. For now, he plans to finish teaching this term.
BYU spokeswoman Carri Jenkins said the decision to let Nielsen go came from the philosophy department.
"The department made the decision because of a recent opinion piece that publicly contradicted and opposed a statement by the First Presidency," Jenkins said. "Such contradiction is in violation of university policy."
In a statement read over pulpits the week before Nielsen's column ran, leaders of The Church of Jesus Christ of Latter-day Saints urged members to support a constitutional amendment banning same-sex marriage and asked them to "express themselves on this urgent matter" to U.S. senators.
Elder Russell M. Nelson of the Quorum of the Twelve Apostles went to Washington to show the church's support for the measure.
Despite that push and a flood of letters from Mormons, the Senate rejected the amendment June 7.
Like thousands of Latter-day Saints, Nielsen chose to express himself on the matter. His stand, however, was in public opposition.
"Further, to say that gay marriage will destroy traditional marriage and the family without giving any reasons why is the fallacy of appealing to fear," Nielsen wrote. "Indeed, once you get past the emotion, it is quite an unfounded claim."
Nielsen's column also criticized church leaders, saying he finds "quite troubling" their statement that God has ordained marriage as a union between one man and one woman - especially given the faith's history with polygamy.
He stressed he sustains the First Presidency and Quorum of the Twelve Apostles but rejected the premise that they are "immune from thoughtful questioning or benevolent criticism."
"In my mind, there is no contradiction between raising some questions and concerns and at the same time sustaining" church leaders, he said Tuesday. "Even though I realize, for the vast majority of church members, those two things are contradictory."
Nielsen maintains he wasn't attacking religious or theological claims, but rather commenting on a moral issue.
Former BYU professor David Knowlton can empathize with Nielsen's position.
Knowlton was denied tenure from the Provo university in 1993 after he criticized the church's missionary program in the independent Sunstone forum.
"Obviously, the decision is unfortunate," said Knowlton, now an associate professor of anthropology at Orem's Utah Valley State College. "I really feel for him and his family because it's a horrible thing. I've been through it."
Nielsen acknowledged the fallout has been rough on him, his wife and his children. He said he never meant to create conflict but added he felt the need to speak out.
The father of four conceded he has endured sleepless nights since the column appeared but reaffirmed Tuesday he is sticking by his views and his religion.
"I'm walking a very fine line here, trying to do what I think is morally correct," Nielsen said, "and at the same time maintain my membership."
Other high-profile firings
* English professor Cecilia Konchar Farr in 1993 after she gave a speech supporting a woman's right to an abortion.
* Anthropologist David Knowlton in 1993 after publishing studies on the church in Latin America.
* English professor Gail Turley Houston in 1996 after she "publicly contradicted" doctrine.
* History professor Steve Epperson in 1996 because he lacked an LDS temple recommend.
- Source: Tribune archives
Nielsen has more questions
Opposition to same-sex marriage isn't the only LDS Church stand Jeffrey Nielsen questions. The part-time Brigham Young University instructor, who will not be rehired for contradicting church statements, said he wants to address other moral and social issues. He urges church leaders to:
* Commission BYU scientists to investigate the nature of the current scientific understanding of same-sex attraction.
* State clearly the the church's position on the past denial of priesthood to blacks.
* Clarify the nature of polygamous teachings in the church, both past and future.
* Reveal "real membership numbers" and churchwide activity rates.
* Allow worthiness interviews between church leaders and teenage members to occur only in the presence of a parent or guardian.
* Permit nonmember or non-tithe-paying parents to attend their children's LDS temple weddings.
- Todd Hollingshead