When the Church of the Good Shepherd in Binghamton, N.Y., left the Episcopal Church over disagreements about what the Bible says about sexuality, the congregation offered to pay for the building in which it worshiped. In return the Episcopal Church sued to seize the building, then sold it for a fraction of the price to someone who turned it into a mosque.

The congregation is one of hundreds that split or altogether left the Episcopal Church—a member of the Anglican Communion found mostly in the United States—after a decades-long dispute over adherence to scripture erupted with the consecration of a partnered gay bishop in 2003. But negotiating who gets church buildings hasn’t been easy. Presiding Bishop Katharine Jefferts Schori said she’d rather have these properties become Baptist churches or even saloons than continue as sanctuaries for fellow Anglicans.

The Episcopalian congregations that want to break away are part of a larger movement of Anglicans world-wide who are concerned by the liberalism of the official New York-based Episcopal Church on sexuality and certain basic tenets such as Jesus’ resurrection. Of the 38 provinces in the global Anglican Communion, 22 have declared themselves in “broken” or “impaired” fellowship with the more liberal American church.

In 2009, breakaway Episcopalians in the U.S. and Canada formed the Anglican Church in North America, which now reports 100,000 members in nearly 1,000 congregations. This group has been formally recognized by some Anglican primates outside of the United States.

Bishop Jefferts Schori says this new Anglican group is encroaching on her church’s jurisdiction, and she has authorized dozens of lawsuits “to protect the assets of the Episcopal Church for the mission of the Episcopal Church.” The Episcopal Church has dedicated $22 million to legal actions against departing clergy, congregations and dioceses, according to Allan Haley, a canon lawyer who has represented a diocese in one such case.

Now the Episcopal Church has upped the ante: It has declared that if congregations break away and buy their sanctuaries, they must disaffiliate from any group that professes to be Anglican.

Rather than agree to this demand to disaffiliate from Anglicanism, Pittsburgh’s All Saints Episcopal Anglican Church last month walked away from the building it had inhabited since 1928. The congregation called the Episcopal Church’s demand “mean-spirited” and an attempt to deny “the freedom of religious affiliation.”

Some other Episcopalians have opted to disaffiliate rather than lose their buildings or spend years in expensive litigation. Two breakaway congregations in Pennsylvania and two in Virginia have promised they will not affiliate with other Anglicans for five years.

For Anglicans, affiliation with a bishop is essential to their identity and to being part of a church. A disaffiliation clause means that bishops can’t make their annual congregational visits to perform baptisms, confirmations and other rites integral to the life of the church, and they can’t encourage or discipline priests. The congregation meanwhile can’t work with local and national church bodies on disaster relief, youth retreats or educational seminars. Clergy members’ insurance and pensions are uncertain. And congregations can’t advertise that they are Anglican or contribute the traditional 10% tithe to the local branch of their denomination.

“It’s unconscionable for a Christian to impose such a condition on a fellow Christian, telling them who they can and can’t worship with and who they can and can’t affiliate with. That violates every Christian precept I know of,” said Mr. Haley, citing St. Paul’s admonition against Christians suing each other in secular courts.

“We can’t sell to an organization that wants to put us out of business,” said Bishop Jefferts Schori, who added that her job is to ensure that “no competing branch of the Anglican Communion impose on the mission strategy” of the Episcopal Church. Indeed she has no complaint with Muslims, Baptists or barkeepers buying Episcopal properties—only fellow Anglicans.

The archbishop of the break-away Anglican Church in North America, Robert Duncan, says his group has no interest in replacing the Episcopal Church. He says he has encouraged participation with Episcopal Dioceses and recently blessed a priest who wanted to return to the Episcopal Church.

Bishop Duncan says that while the ongoing litigation over property is “unseemly and scandalous,” the new disaffiliation clauses are even worse: “You can ask me to give away what I have and I’ll give it away. But don’t demand of me that I abandon the tenets of my faith.”

Ms. Hemingway is a writer in Washington, D.C.

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