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Updated at 6:44 p.m. ET

The U.S. Supreme Court has carved out a major exception to the nation's fair employment laws. In a 7-2 vote, the court ruled on Wednesday that the country's civil rights laws barring discrimination on the job do not apply to most lay teachers at religious elementary schools.

The case was brought by two fifth-grade teachers at California parochial schools who were fired from their job. Agnes Morrissey-Berru claimed age discrimination, and Kristen Biel said she was fired after she told her superior she had been diagnosed with breast cancer and would need some time off. If true, that would violate the Americans with Disabilities Act.

The schools denied the allegations but maintained that regardless, federal employment laws do not apply to their teachers because they all are required to teach religion for 40 minutes a day in addition to other academic subjects.

Now the Supreme Court has agreed.

Writing for the seven-justice majority, Justice Samuel Alito said "state interference" in religious education would violate the free exercise of religion guaranteed by the First Amendment.

"The religious education and formation of students is the very reason for the existence of most private religious schools, and therefore the selection and supervision of the teachers upon whom the schools rely to do this work lie at the core of their mission," Alito wrote.

As the court saw it, federal courts are not allowed to settle employment disputes involving teachers similar to those in these cases because the religious schools are making "internal management decisions" that are "essential to the institution's religious mission."

The lower courts have long considered ministers exempt from the nation's employment laws, but lay teachers have been treated differently.

In 2012, the Supreme Court ruled unanimously that a fourth-grade teacher at a Lutheran school who was commissioned as a minister could not sue over her firing.

Wednesday's decision expanded that exception to include teachers who lacked religious titles and training, potentially stripping fair employment protections from many of the roughly 149,000 teachers at religious elementary schools, where they frequently teach religion alongside other subjects.

As to the nearly 200,000 teachers at religious middle and high schools as well as schools that include both primary and secondary education, it is not entirely clear what will happen.

Stanford Law School professor Michael McConnell said, "If there's a teacher that does not have religious responsibilities, I think that teacher falls outside the exception. So, for example, a physics teacher in high school would not be covered."

But what if the physics teacher were also a homeroom teacher who leads the class in prayer or accompanies the class to Mass?

"That's a fair question, and it's certainly an open question after this opinion," said University of Virginia School of Law professor Douglas Laycock, who signed a brief siding with the religious schools.

Alito pointed out that the Archdiocese of Los Angeles, where both of the fired teachers in these cases worked, considers all its teachers catechists "responsible for the faith formation of the students in their charge each day" and expects teachers to infuse Catholic values "through all subject areas."

Laycock conceded that as a result of Wednesday's opinion, there may be injustices in some cases, with teachers being fired over forbidden criteria such as age or disability, only to have no recourse in courts.

"We tolerate the occasional abuses because the cost of judges and juries second-guessing every personnel decision ... are on the whole much greater," Laycock said.

The ruling leaving lay teachers without anti-discrimination protections was one of three major decisions in recent weeks that re-balance the law when it comes to the separation of church and state.

In a separate decision Wednesday, also 7-2, the court upheld a Trump administration rule that allows employers with religious or moral objections to opt out of providing birth control coverage for their employees. The decision is expected to strip coverage from more than 100,000 women.

And last week, the court effectively invalidated state constitutional provisions in most states that barred taxpayer funds from going to private religious schools.

Stanford law professor Jeffrey Fisher, who represented the fired teachers before the court, believes this trilogy of opinions will have major consequences.

"The court has issued three big decisions in favor of its view of religious liberty in a way that makes this perhaps the most pro-religion court in the history of our country," he said.

For much of the 20th century, the Supreme Court's legal opinions enforced a strict separation between church and state. But as the court has grown more conservative in the last two decades, it has increasingly abandoned that notion. Now the justices tend to focus their opinions on protecting the free exercise of religion and requiring greater accommodations by the government of religious activity.

"I do think there's a tone in these opinions that religious groups are not being taken seriously enough," said University of Chicago law professor David Strauss, a co-editor of The Supreme Court Review, "a tone that in our society today religious groups are looked down on. ... They're not protected to the extent other groups are protected."

In short, the Supreme Court majority now views religious groups as victims of discrimination.

Strauss added that while religious institutions do have legitimate concerns, "it's not a coincidence that the cases before the court involved age discrimination and discrimination on the basis of disability, because those are two areas in which employers, either in fact or because they're in the grip of stereotypes, think they have economic incentives to fire employees."

Justices, of course, are to some extent the product of their life experiences as well as of their education. Six of the nine were raised Catholic, and five of them were educated at parochial schools.

Alito, the only one of the court's conservatives not educated in religious schools, authored the opinion in the teacher case. Justice Clarence Thomas, a onetime seminarian, wrote the birth control opinion.

In the teacher case, Justice Sonia Sotomayor, who was also educated at parochial schools, wrote the dissent for herself and Justice Ruth Bader Ginsburg, calling the decision "profoundly unfair" for "permitting religious entities to discriminate widely and with impunity for reasons wholly divorced from religious beliefs," even as the court has "lamented a perceived 'discrimination against religion' " in recent opinions.

Sotomayor pointed to specific provisions that Congress wrote into the nation's anti-discrimination laws so that churches, synagogues, mosques and other houses of worship could choose their ministers, rabbis, imams and other religious leaders without interference from the government.

In expanding those exceptions beyond their "historic narrowness," she said, the court majority has leveled a "constitutional broadside" at hundreds of thousands of employees who work not just at religious schools but also religious hospitals, charities and universities.

The court did not address the potentially expansive implications of its decision. But if Sotomayor is right, millions of employees at religious organizations could eventually find themselves excluded from the protections of federal fair employment laws, too.

Thomas seemed to welcome such a possibility. He joined the opinion in full but also wrote separately for himself and Justice Neil Gorsuch to say that courts shouldn't second-guess when religious organizations sincerely claim that their employees are carrying out the religious mission of the organization, and are thus "ministerial" and exempted from fair employment protections.

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