From homeland security to healthcare, the federal government now has the power to reach further than ever into American society. But so far, the feds have sensibly stayed out of the business of appointing religious leaders.

Now, in a stunning about-face, the Obama Administration has urged the Supreme Court to allow courts to decide virtually any dispute between a church and its ministers. In the administration’s view, juries and judges, not congregations and bishops, should have the final say on who is fit for religious ministry. Fundamental questions of theology would be resolved in the same way as slip-and-fall cases. Plaintiffs’ lawyers would go into a religious feeding frenzy.

The DOJ made this astounding declaration in its brief for a Supreme Court case called Hosanna-Tabor Evangelical Lutheran Church and School v. Equal Employment Opportunity Commission, which some observers have called the most important religious freedom case in 20 years.

The case started when Cheryl Perich, a former teacher at a church-run grade school, wanted to return from a disability-related leave of absence. The school, which is part of the Lutheran Church-Missouri Synod, had far exceeded its legal obligations in accommodating her disability. But when some board members expressed concern that she wasn’t medically ready for work, she threatened to sue for discrimination.

That threat had serious religious implications. Like many denominations, the Lutheran Church has long taught that Christians should resolve their disputes within the church, not in secular courts. Perich’s threat publicly rejected that teaching.

Perich, moreover, wasn’t just any employee, but a “called” teacher. Besides teaching secular subjects like science and English, she was a Lutheran “commissioned minister” who was expected to lead her students in prayer, to provide their primary religious instruction, and lead them in worship. In her church’s view, Perich’s refusal to follow Lutheran teaching on dispute resolution made it impossible for her to carry out these religious duties. Accordingly, the congregation voted to rescind her call.

Perich and the Equal Employment Opportunity Commission (EEOC) responded by suing the church. A federal district court dismissed the case, finding that it would be inappropriate for judges to second-guess a church’s decision about who should carry out important religious duties. After an appeals court reversed that outcome, the U.S. Supreme Court agreed to hear the case, which is set for argument on October 5.

The key issue in the case is an obscure doctrine with big consequences. The doctrine, called the “ministerial exception,” bars most employment-related lawsuits brought against religious organizations by employees performing religious functions.

The point of the ministerial exception isn’t that churches always behave well (they don’t), or that they’re above the law (they’re not). Rather, it recognizes if ministerial employees could sue for discrimination, courts would need to determine whether religious organizations had made the “right” decisions about hiring and firing their ministers. Those kinds of essentially religious decisions are above secular courts’ pay grade.

The lower courts have acknowledged the ministerial exception for forty years. The EEOC’s own compliance manual acknowledges it. So do Americans United for Separation of Church and State and the ACLU, which filed a friend-of-the-court brief against the church. Until last month, both sides assumed that the question before the court was whether the ministerial exception applied to Perich-not whether it exists.

As we explained in our brief for Hosanna-Tabor, “This would be a revolution in relations between church and state.”

This isn’t the first time the Obama administration has sought to control religious communities’ decisions about their employees. Last month, the Department of Health and Human Services (HHS) issued new guidelines listing “preventative care” benefits for women that all insurance plans must cover, without copay or deductible. These included every FDA-approved mode of sterilization and contraception, including emergency contraceptives that can destroy fertilized eggs. The only employers exempt from this requirement are churches and religious orders – but only if they don’t help or hire people outside their own faith. As a result, thousands of religious schools, hospitals, and other charities must now choose between breaking the law and violating their consciences.

If the Supreme Court buys the DOJ’s argument, many religious communities will face a similarly stark choice: either accept ministers that they consider unfit, or endure endless litigation. The liability would be crippling – not only for churches, but for religious liberty.

William P. Mumma is the president of the Becket Fund, a non-profit, public- interest law firm that defends religious liberty.

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