“It’s heartbreaking for me to see my church drawing this line in the sand, which leaves faithful L.G.B.T. members with an impossible choice: They can either be excluded from lifelong love and companionship, or excluded from the blessings of the church,” she said.

Affirmation, an organization for gay Mormons and their families, said it had received “a flood of reactions” from members expressing “grief, shock, disbelief and spiritual confusion.” The group said on its website that, “Many L.G.B.T.Q. members of the church have striven to keep the faith, some of them even raising their children in the church.”

Mormons, while generally socially conservative, are increasingly accepting of gay relationships, reflecting broader trends in American life that affect even members of the most traditional faiths. A new study released this week by the Pew Research Center on Religion & Public Life found that 36 percent of Mormons agreed in 2014 that homosexuality should be accepted by society, up from 24 percent in 2007. But, the study notes, Mormons continue to be among the least accepting of homosexuality when compared with other religious believers.

The church has lobbied against laws legalizing same-sex unions, but has also in recent years supported laws intended to protect gay people from discrimination. In March, leaders at the church’s headquarters in Salt Lake City helped to pass a bill known as the “Utah compromise,” which bans discrimination against lesbian, gay, bisexual and transgender people in housing and employment but protects religious institutions that do not condone gay relationships.

One top Mormon official recently delivered a major address saying that public officials like Kim Davis, the Rowan County, Ky., clerk who went to jail after refusing to issue marriage licenses, must follow the law despite their religious opposition to gay marriage.

The handbook had already explained that a disciplinary council “may be necessary” for Mormons who engaged in “homosexual relations.” The new policy said a disciplinary council was “mandatory” for Mormons in “same-gender” marriages and “may be necessary” for same-sex couples who are cohabiting but not married.

Disciplinary councils are convened for Mormons accused of serious transgressions, including murder, rape, sexual abuse, adultery and apostasy. A disciplinary council is a formal church proceeding that could result in excommunication.