UPDATE: see below
The New York Times reported on a decision by the Supreme Court, excerpted below:
In what may be its most significant religious liberty decision in two decades, the Supreme Court on Wednesday for the first time recognized a “ministerial exception” to employment discrimination laws, saying that churches and other religious groups must be free to choose and dismiss their leaders without government interference.
“The interest of society in the enforcement of employment discrimination statutes is undoubtedly important,” Chief Justice John G. Roberts Jr. wrote in a decision that was surprising in both its sweep and its unanimity. “But so, too, is the interest of religious groups in choosing who will preach their beliefs, teach their faith and carry out their mission.”
...the ruling will have concrete consequences for countless people employed by religious groups to perform religious work. In addition to ministers, priests, rabbis and other religious leaders, the decision appears to encompass, for instance, at least those teachers in religious schools with formal religious training who are charged with instructing students about religious matters.
UPDATE: commentary on the decision at Religion Clause
If the Religion Clauses broadly preclude the government from imposing a minister on a church, presumably they likewise preclude the government from preventing a church from hiring particular clergy. Does this mean that the federal government may not deport an alien who is in the United States illegally when that individual has been chosen to be the minister of a church? Does the principle preclude the state from arresting a minister who is charged with criminal activity because doing so would deprive a church of its chosen religious leader? Where the Constitution was most concerned about autonomy-- Congress' autonomy from interference by the Executive Branch-- the Constitution did create at least limited immunity from arrest.
And if church autonomy precludes governmental interference in selection of those who will personify its beliefs, does it also preclude governmental interference in the design of church buildings that personify the Church's image to its adherents and to outsiders? If so, how does that limit zoning laws? Indeed Justice Alito's explanation of church autonomy in his concurring opinion suggests a principle broader than just selection of clergy:The First Amendment protects the freedom of religious groups to engage in certain key religious activities, including the conducting of worship services and other religious ceremonies and rituals, as well as the critical process of communicating the faith.Finally, by holding that the ministerial exception is constitutionally required, the Court seems to call for its application at least in every kind of litigation that deals with hiring or firing of a minister. So while the court says it is not deciding the issue, it seems difficult to envision a court being able to adjudicate a breach of contract claim by a fired minister against his or her church without the court also interfering in the church's choice of its leaders.