Assaults on religious freedom are becoming ever more common. Barely a day goes by without news of a baker punished for not catering a same-sex wedding, a Catholic adoption service banned from limiting its services to married couples, or companies that are run in accordance Christian values being forced to provide health insurance policies that cover abortion.

Troubling as those developments are, they pale in comparison to ultimate threat to religious liberty in the U.S., the desire by many on the secular left to deprive churches and other religious organizations of the right to choose their own clergy free from government interference.

While that threat may seem farfetched, as I described in my new book, “Lawless: The Obama Administration’s Unprecedented Assault on the Constitution and the Rule of Law,” no lesser power than the Obama administration has weighed in, arguing to the Supreme Court that the Free Exercise Clause does not protect the right of religious bodies to decide who should serve as their priest, minister, or rabbi.

Until President Obama was elected president, federal courts consistently, indeed unanimously, held the constitution’s Religion Clauses protect the right of religious organizations to choose their religious staff free from the interference of secular law.

The right to choose religious staff became known as the “ministerial exception,” and the only real controversy in the courts was how broadly the exception should apply.

It obviously applied to actual clergy—ministers, priests, imams, and rabbis— but what about church organists? Sunday school teachers? Administrative staff?

The issue finally reached the Supreme Court in a case involving the Hosanna-Tabor evangelical school, a private elementary school affiliated with the Lutheran Church–Missouri Synod, and former Hosanna-Tabor teacher Cheryl Perich. Perich had taught secular and religious subjects at the school and occasionally led chapel.

After being fired by the school, Perich sued for discrimination based on disability, and the federal Equal Employment Opportunity Commission took up her case. The Sixth Court of Appeals held that because Perich’s duties mostly were the same as those of lay teachers, the ministerial exception did not apply to her job. So Hosanna-Tabor presented the Supreme Court with a perfect opportunity to clarify the scope of the ministerial exception.

But first the Court had to contend with a radical, unexpected argument from the federal government. The Obama Justice Department argued not just that Perich’s job did not qualify for the ministerial exception, but that the ministerial exception should be rejected entirely. So, for example, a very liberal jurisdiction such as San Francisco could require the Catholic Church to hire male nuns or female priests, and the church would have no constitutionally valid freedom of religion defense.

To say that the government’s position was outside the mainstream would be a gross understatement. Though opposition to the ministerial exception has some purchase in the left-wing corridors of the legal academy, from the time the exception first explicitly surfaced in 1972, every federal court that had considered whether to adopt the exception had done so.

When the case reached the Supreme Court, the justices were incredulous at the government’s position that religious organizations get no more constitutional protection than any other employer that promotes a point of view.

Chief Justice John Roberts asked the government’s attorney, “Is the issue we are talking about here in the view of the United States any different than any other group of people who get together for an expressive right?” The attorney answered, “We think the basic contours of the inquiry are not different.” “That’s extraordinary,” Justice Antonin Scalia chimed in. Even Justice Elena Kagan, a liberal Obama appointee, piled on. “I, too, find that amazing,” she said.

Not surprisingly, the Court ruled 9-0 against the administration, endorsing the ministerial exception and holding that it protected Hosanna-Tabor from Perich’s lawsuit.

That’s the good news.

The bad news is that, even though the argument failed to get any votes this time, the issue will inevitably come back to the Supreme Court in the future. By then, restrictions on religious freedom in the name of prohibiting “discrimination” may have become so commonplace that doing away with the ministerial exception could seem like the next logical step.

So the next time someone tells you that there is no war on religious freedom in the United States, ask them if they’ve heard of a case called Hosanna-Tabor.