Eugene Volokh points to an interesting case, Ben-Levi v. Brown, which challenged North Carolina prison regulations governing religious study. North Carolina generally allows group religious study by its inmates, but for Jews it requires either a minyan (ten adult male Jews) or the presence of a Rabbi. As one can imagine, either can be difficult to obtain in North Carolina penitentiaries, and Ben-Levi sued complaining of a First Amendment violation.
Like Professor Volokh (and Justice Alito), it seems to me that this is a clear Free Exercise violation. The state of North Carolina has no business telling Jews how they can and cannot practice Judaism. No doubt for many Jews the minyan requirement is a prerequisite to observing certain religious rites. But it is up to the Jew in question, not the state, to determine whether and how that rule applies to their individual circumstances. That's the essence of church/state separation: the state has no business interjecting itself into questions of theology. A general policy restricting group religious study (North Carolina mentioned a concern about it becoming a cloak for gang meetings) might present a tougher case, but there is no valid argument I can see for creating a specially restrictive rule for Jews -- even (especially) one based on North Carolina's interpretation of Jewish religious doctrine.
Unfortunately, the Supreme Court declined to hear the case (over a dissent by Justice Alito). Note that such a decision, while upholding the lower court rejection of Ben-Levi's claim, does not itself establish any precedent. Far more cases are appealed to the Supreme Court than it elects to hear, so one should be very cautious about reading too much into it. But a legitimate tsk-tsk can go out to the District Court and Fourth Circuit, who seem to have gotten it badly wrong here.