After weeks of cross-examination, witness lists and wrangling over admissible evidence, the Rev. Frank Schaefer stood in the gymnasium of a rural Methodist retreat center to answer a charge: Did he violate his faith when he officiated at his son’s same-sex wedding?

By the end of the day Monday, the rare jury of 13 Methodist pastors had found Schaefer guilty on two charges: “conducting a ceremony that celebrates same-sex unions” and “disobedience to order and discipline of the Methodist Church.”

On Tuesday morning, the jury reconvened to devise Schaefer’s penalty for agreeing in 2006 to officiate at the marriage of his son, Tim, who earlier had contemplated suicide over his homosexuality. The penalty in past similar cases has ranged from a short suspension to defrocking.

First to testify was William Bailey, a longtime member of the Zion United Methodist Church, who said he and Schaefer over the years had “agreed to disagree” about literalism and scripture.

“I believe in the Bible, and the [Methodist Book of Discipline] is enforcing the Bible and the Ten Commandments,” said Bailey from a witness stand before some 150 rapt listeners — mostly advocates for gay rights. “Violating a rule makes me very, very stubborn. Because if I violate a rule, I expect to be punished, and I expect nothing else from our church.”

Christina Watson, a newer member who was overseeing Christian education at the church, broke into tears as she described Schaefer telling her that the Methodist Book of Discipline “was just guidelines, that it didn’t have to be followed.” She said she took her family out of the church this fall.

In a nation where places of worship tend increasingly to line up on one side or the other on hot-button issues, something beyond Schaefer himself seemed to be on trial: the possibility of a spiritual middle ground.

Schaefer and other members of Zion United Methodist Church, in the small eastern Pennsylvania town of Lebanon, had largely tried to avoid the divisive topic of sexuality and focus on God. Now, the issue is unavoidable.

“I see you on both sides. I see your tears, and I hurt for every member of this church that is in pain. You have to remember — God is in control,” pastoral assistant Clydette Overturf preached Sunday to about 60 congregants, many with tears streaming down their cheeks. “We are a family. Families have struggles. We aren’t the first church to hurt, and we won’t be the last.”

Indeed, Schaefer is the first among five Methodist ministers to be accused by church officials over the past year of possibly violating church doctrine on gay rights. The other four could also face church trials. The cases, which are being closely watched by advocates on both sides, represent perhaps the biggest flare-up in recent years in mainline Protestantism over the issue of homosexuality. At 8.3 million members, Methodists are the second-largest group of Protestants in the United States.

A church trial is unusual, as is the sight of a pastor as a “defendant” of his ministry to his own son. The Schaefer family is also atypical in that three of the pastor’s four children are gay.

At the same time, parts of the story unfolding at Zion are very familiar in American religion: a church torn apart by personality clashes or power struggles about routine matters, including whether to keep the service traditional or make it more contemporary and who gets hired or fired.

Schaefer’s collision with half of his congregation was in some ways inevitable.

He grew up in a conservative evangelical home in Germany and believed as a younger adult that “homosexuality is incompatible with Christian teaching,” he said in an interview, using the terminology of the Methodist Book of Discipline. After studying at a theologically diverse seminary, he became convinced that there were different ways to read scripture. But when he wound up being called to a rural, more traditional part of the country, he realized he had a choice to make.

“It’s a very conservative area. You have to make a choice as a minister: If I am going to be a shepherd to these people, I can never talk about it. Which I didn’t,” he said.

This was something of the unspoken rule in a congregation where people knew views were mixed. “I’m like Switzerland. We try to keep it neutral,” said Jackie Krezmien, who came to Zion about six years ago.

Schaefer didn’t talk about it at home, either. Tim Schaefer, the oldest of Schaefer’s three sons, says he remembers suspecting that his parents wouldn’t reject him, but he wasn’t sure.

Schaefer began at Zion in 2002 after serving another eastern Pennsylvania church. That was two years after a parent called the pastor anonymously to tell him Tim, then 16, was gay and considering suicide. Schaefer and his wife asked their son point-blank.

“What sticks in my mind, he was so upset not that I was gay, but that I had planned to wait to leave the house before saying anything,” said Tim Schaefer, who lives in Massachusetts and is no longer married.

“My wife and I lost it in tears. We hugged him. We told him we loved him so much,” the pastor said separately in a phone interview. “To me, this was definitely the proof — he did not choose this.”

But even as Schaefer thought he was being silent on the issue in church, some longtime conservative members noticed a change from previous pastors when he arrived 11 years ago.

He started a second, contemporary service and began focusing heavily on it in an attempt to grow the church. He wasn’t hesitant to change the structure of the service and music, and “there was a drift from scripture,” said Bonnie Leibold, the assistant choir director at Zion for 30 years before leaving over the dispute.

“His preaching was unorthodox. It’s hard to pinpoint anything. The church just felt like it was changing,” said Kitty Mease, 85, who left two years ago after a half-century at Zion. While Schaefer didn’t preach explicitly on homosexuality, she said, general comments about inclusion felt coercive in a traditional community.

“He was trying to change our views. Some of this we knew — though we didn’t know the extent that the entire family was [part of] this other lifestyle apparently,” Mease said.

And in 2006 came Tim’s request. He called his father to say he was engaged and asked his father to marry him. Both knew the moment was fraught in Methodism.

“I thought about the severity of what I had done,” the minister told the court Monday. But considering his son’s previous emotional struggles, Schaefer said that when Tim asked his father to affirm his marriage, “seeing my son needing ministry, asking me for help. . . . I couldn’t pass on the other side of the road like a Levite to preserve a rule. All I saw was love for my son.”

The Methodist Church, like the rest of mainline Protestantism, has been wrestling with issues surrounding gay rights for decades. It has added affirmations about the dignity of gays and lesbians and the importance of pastors to minister to them, but unlike some other mainline denominations, the Methodist Church has not expanded gay rights on things such as marriage and allowing clergy to be openly gay.

In reality, many bishops practice a don’t ask, don’t tell policy, and many Methodist churches are led by gay clergy.

There were at least four Methodist Church trials between 1998 and 2011 for clergy accused of performing same-sex weddings or of being openly gay, and all were convicted. One pastor was tried twice.

But five new potential cases have appeared in just the past year or so as more pastors have worked to move the issue out of the closet. Two other pastors, like Schaefer, married their children — including Thomas Ogletree, the esteemed retired dean of Yale University Divinity School.

On an early spring day in 2007, in front of about 150 people in a Massachusetts restaurant, Schaefer presided over his son’s wedding. He made no announcement of his role in the wedding to his congregation, though Leibold and others say rumors about his participation existed for years.

While Leibold, Mease and others say they don’t support gay marriage, they say it wasn’t a key issue as tensions continued to build. Some of them went to the superintendent, or regional leader, and the bishop with complaints about how decisions were made.

“They kept telling us, ‘You have to resolve this yourself,’ ” Leibold said. But the bishop said, “ ‘If you bring me something [like a rule violation], I can address that.’ ”

But Overturf says the new, more inclusive language was a big factor. “[Sexuality] was an issue. The rest is scapegoating,” she said.

Over the years, the tensions built. About half the church’s 250 members have left since spring because they disagreed with Schaefer officiating his son’s wedding or with Methodist officials for pursuing him or because they were tired of the acrimony.

The conflict hit its zenith this spring, when Schaefer removed the longtime choir director, a member of the more traditional group. Within days, her son secured the 2007 wedding certificate from Massachusetts and sent it to the bishop within a few weeks of the statute of limitations running out.

Under trial rules, her son’s name was kept private until Monday, when Jon Boger, a strapping Navy lieutenant commander, wept on the stand as he described his time away from his family — because he was keeping his oath to the service. Schaefer must also keep his oath, Boger said.

“You have a choice. If you violate it it’s your decision,” Boger said.

Boger said he has “no issue” with people who are gay — though he opposes same-sex marriage.

“I do think homosexuality is unnatural and immoral and sinful. But you still need to treat people with dignity and respect. It’s not an issue,” Boger said.

Schaefer believes that Methodism’s governing documents are contradictory. The Book of Discipline calls pastors to minister equally to all people, he said in an interview. Methodism’s constitution demands inclusiveness.

At its root, such conflicts are about whether scripture is fixed in the past or continues to be revealed, said Scott Campbell, a Harvard University chaplain and counsel to one past and one current pastor facing trial for officiating at a gay marriage. “Those of us who want to say God is continually making things new see this as one of the manifestations of this newness.”

Schaefer and other trial participants were prohibited by church rules from commenting on the verdict Monday.

On Sunday, the people of Zion were still trying to maintain that middle road, the one disappearing from much of American religion. Even as their pastor was not present, with his attorneys preparing for a church trial, the congregation members tried to stick with the routine. The bulletin led with an item urging people to decorate the sanctuary for Advent, and services started with an announcement about ordering poinsettias.

People who may disagree about gay marriage but want to stay together as a church belted out contemporary Christian rock, and when Overturf said, “God is good!” the congregation responded, “All the time!” The talk was not about sexuality, but about prayer.

“We pray, God, you use this opportunity to help people see that you are alive,” said a man leading a mid-service prayer. “Not everything goes the way we want. The answer is sometimes yes and sometimes no. But you’re always there.”