Matt Aune said he and his partner, Derek Jones, were confronted by guards after they hugged and kissed on the plaza.
Former Salt Lake City Councilwoman Deeda Seed helped organize Sunday's kiss-in, which occurred on public property.
The Salt Lake Tribune reported on its Web site that heterosexual and gay couples exchanged small kisses and pecks at the plaza's south entrance, which faces downtown. Church security was present, but the Deseret News of Salt Lake City reported on its Web site that no altercations occurred.
The church has been the target of protests over its support of a ban on gay marriage in California.
Aune said he and his partner, Jones, were walking home from a concert nearby on Thursday night, cutting through the plaza near the Salt Lake City Mormon temple.
Aune, 28, said he gave Jones, 25, a hug and kiss and that the two were then approached by a security guard, who asked them to leave, telling them they were being inappropriate and that public displays of affection aren't allowed on the property. He said other guards arrived and the men were handcuffed.
"We asked what we were doing wrong," Aune told The Associated Press.
Church spokeswoman Kim Farah said in a statement Friday that the men were "politely asked to stop engaging in inappropriate behavior - just as any other couple would have been."
"They became argumentative and used profanity and refused to leave the property," she said. The church did not immediately respond to a request for more comment.
Police later arrived and both men were cited with misdemeanor trespassing, Salt Lake City Police Sgt. Robin Snyder said.
"It doesn't matter what they were asked to leave for," Snyder said. "If they are asked to leave and don't they are ... trespassing."