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The Supreme Court appeared sharply divided Wednesday on whether a church school can be sued over an employee's discrimination complaint, raising questions that pit the constitutional separation of church and state against the government's interest in protecting people from discrimination and retaliation.

This is the first time the high court has looked at a doctrine developed in lower court rulings that the First Amendment's guarantee of freedom of religion shields churches and their operations from the reach of anti-discrimination laws when dealing with religious employees, so religious groups and civil rights advocates are watching closely.

Churches have argued that a decision against the Hosanna-Tabor Evangelical Lutheran Church and School of Redford, Mich., could lead to government interference in the internal operations of religious organizations. But civil rights and employee rights organizations say churches are trying to stretch protections designed for religious workers beyond their intended purpose to shield their groups from the discrimination and retaliation claims of workers like former teacher Cheryl Perich in this case.

The issue in dispute is whether a government agency, the federal Equal Employment Opportunity Commission, has the right to sue the school on Perich's behalf for firing her after she complained of discrimination under the Americans With Disabilities Act.

Perich was promoted from a temporary lay teacher to a "called" teacher in 2000 at the school by a vote of the church's congregation and hired as a commissioned minister. She taught secular classes, as well as a religious class four days a week. She also occasionally led chapel service.

She got sick in 2004 but tried to return to work from disability leave despite being diagnosed with narcolepsy. The school said she couldn't return because they had hired a substitute for that year. They fired her and removed her from the church ministry after she showed up at the school and threatened to sue to get her job back.

Perich complained to the EEOC, which sued the church for violations of the disabilities act.

A federal judge threw out the lawsuit on grounds that Perich fell under the ADA's ministerial exception, which keeps the government from interfering with church affairs. But the 6th U.S. Circuit Court of Appeals reinstated her lawsuit, saying Perich's "primary function was teaching secular subjects" so the ministerial exception didn't apply.

Chief Justice John Roberts seemed to disagree with that decision during oral arguments before the court Wednesday.

"The pope is a head of state carrying out secular functions, right? Those are important. So he is not a minister?" Roberts asked Perich's lawyer, Walter Dellinger, in disbelief.

The church's lawyer, Douglas Laycock, argued that because Perich was a minister as well as a teacher at the now-closed school, and those jobs overlapped, the government could not get involved in the church's hiring and firing decisions. "These decisions are committed to churches by separation of church and state," Laycock said.

The First Amendment of the Constitution bars the government from impeding the free exercise of religion.

But what if a church claims its religious beliefs include illegal activities such as sexually exploiting children or smoking illegal narcotics? asked Justice Sonia Sotomayor.

"Regardless of whether it's a religious belief or not, doesn't society have a right at some point to say certain conduct is unacceptable?" she said. "And once we say that's unacceptable, can and why shouldn't we protect the people who are doing what the law requires, i.e., reporting it?"

Laycock responded: "If the government's interest is in protecting ministers from discrimination, we are squarely within the heart of the ministerial exception. If the government's interest is something quite different from that, like protecting the children, then you can assess whether that government interest is sufficiently compelling to justify interfering with the relationship between the church and its ministers."

The church would be able to argue those questions if the case were allowed to go to court, Justice Anthony Kennedy said. "I'm saying if there are some substantial issues the church has, that can be litigated in EEOC hearings," Kennedy said. Perich "was fired simply for asking for a hearing."

But Justice Antonin Scalia said, "It's none of the business of the government to decide what the substantial interest of the church is."

Courts normally give a lot of deference to a church's decision about who is a minister and who is not, Justice Samuel Alito said. If they don't, he said, the government then would have to get into the business of deciding who is an official minister of a church and who is not and what the beliefs of a church are. The church said in court papers it fired her because suing the church in court is against their religious teachings.

So you'd have to get into "what did Martin Luther actually say about suing the church? ... Is this really a central tenet of Lutheranism? Isn't that the problem" with delving into this analysis, Alito said.

But the government already does that, Justice Stephen Breyer said. "I don't see how you can avoid going into religion to some degree. You have to decide if this is really a minister, for example, and what kind of minister. That gets you right involved," Breyer said.

The Obama administration said a ruling for Perich would not allow a woman to sue the Catholic church for discrimination for not allowing a woman to become a Catholic priest.

"The government's general interest in eradicating discrimination in the workplace is simply not sufficient to justify changing the way that the Catholic Church chooses its priests, based on gender roles that are rooted in religious doctrine. But the interests in this case are quite different. The government has a compelling and indeed overriding interest in ensuring that individuals are not prevented from coming to the government with information about illegal conduct," Justice Department lawyer Leondra Kruger said.

The court will rule in the spring.

The case is Hosanna-Tabor Evangelical Lutheran Church & School v. Equal Employment Opportunity Commission, 10-553.

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