BOSTON — The historic Church of the Covenant just off the city’s Public Garden has been an important place for Anne Crane and Sarah Perreault.

The lesbian couple had their first date there in the late 1970s, and by the time Massachusetts legalized same-sex marriage in 2003, the two had been active members for more than 25 years. A church wedding seemed the obvious choice.

But it was complicated. The Church of the Covenant is dually aligned with the United Church of Christ, which allows same-sex couples to be married, and the Presbyterian Church (USA), which does not.

“It’s painful to know that the church that I’ve been a part of all my life does not recognize our relationship as being a legitimate marriage,” Crane told the PBS program Religion & Ethics NewsWeekly.

When the couple married in 2004, the Church of the Covenant brought in a retired UCC minister to conduct the ceremony, while the Presbyterian side officially stayed out of it. The couple said their wedding was beautiful, even though it was not quite everything they would have planned.

“I felt badly because there were people that we would have liked to include in our ceremony who could not participate because they were ordained Presbyterian clergy,” Perreault said. “There was a real loss there.”

For decades, mainline denominations have been wrestling with issues surrounding homosexuality: whether to ordain gay clergy and whether to recognize — and bless — same-sex unions.

Now that six states have legalized gay marriage, these battles are taking on a new urgency. In the Episcopal Church, for example, bishops from those six states are seeking permission to alter age-old marriage rites for use at gay and lesbian weddings.

That, in turn, has prompted pressure on conservatives to hold the line.

“The church shouldn’t just go along with what the wider society demands of it,” said Mark Tooley, president of the Institute on Religion and Democracy, a conservative advocacy group that fights gay rights moves within mainline denominations. “The church is ideally supposed to be faithful to timeless teachings that have been presented to the church through its Scripture and through its traditions.”

Currently, while Unitarians and the UCC sanction gay marriages, other mainline denominations don’t officially allow them. Clergy who participate in same-sex weddings could face church trials and even risk being defrocked.

In the United Methodist Church, retired pastor Richard Harding has a long history of activism for gay rights. He helped found Reconciling Retired Clergy, a network of retired pastors willing to perform gay marriages.

“There’s not a whole lot that they can do to (us) retired clergy, and there’s a whole lot they can do to active clergy,” said Harding, 83. “And that’s why we’re stepping in.”

The Rev. Jennifer Wegter-McNelly, the Church of the Covenant’s interim pastor, says her congregation is in a difficult position trying to maintain support for gay members while still respecting denominational rules.

“We have a long history, and we’re very active, and so I think there is a lot of really thoughtful hard conversation about how do we be prophetic and remain faithful and connected to the churches that are our larger community,” she said.

In the Episcopal Church, which also doesn’t officially allow gay marriage, many parishes aren’t performing any weddings — gay or straight. Instead, said the Rev. Pam Werntz of Boston’s Emmanuel Episcopal Church, they provide a blessing for couples who are married by the state.

“That could happen separately, it could happen at the courthouse and then a couple comes here for the ceremony, or it can happen in the same ceremony where a justice of the peace presides over the first part of the service and a priest presides over the blessing and, often, Eucharist celebration,” she said.

The compromise may have helped circumvent some of the denominational difficulties, but Werntz said it was still painful for many members.

“There were people that left the church feeling a lot of sorrow and betrayal that the Episcopal Church couldn’t move as fast as I think it needed to move when same-sex marriage was legalized,” she said.

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While mainline pastors continue to be conflicted over the issue, those who support gay marriage still appear to be in the minority.

According to a recent survey by Public Religion Research, mainline clergy are generally more supportive of gay rights than Americans as a whole, althoughonly one-third of mainline pastors endorse gay marriage; that number is just about the same for Americans overall.

“Often people in wider society are very surprised to learn that the mainline churches don’t already accept same-sex marriage, because these churches, at least for the last 50, 60 years or more have been on the liberal side of social issues,” Tooley said. “But they have hung back on the marriage issue.”

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In the Presbyterian Church (USA), the Rev. Mary Holder Naegeli is among those urging the denomination to maintain its stand. “Homosexual practice is not God’s design for humanity,” she said. “Clear prohibitions in the Scripture make homosexual practice a sin. Homosexual marriage makes permanent a situation that God wants to redeem.”

But for clergy like Wegter-McNelly, the debate over homosexuality is not a theoretical exercise; it comes down to her pastoral care of her parishioners.

“Here gay marriage isn’t an abstract issue. It’s not a political issue.” she said. “To tell people that this community that is the compass for your life is not going to bless and support you in your intimate relationship is kind of an impossibility.”