You’d think that there wouldn’t need be a court case deciding this, but now there is, Myers v. City of Chicago (N.D. Ill. Sept. 12, 2012).
The question was whether a fraternity could qualify for a special zoning rule applicable to a “convent or monastery,” defined as housing for “persons (such as nuns or monks) under religious vows.” The court said no, despite the argument that the fraternity’s mission statement — “In the Service of God and Man” — was a “religious vow” that the fraternity members took. Whether it’s permissible for the government to preferentially exempt religious (but not secular) group living from zoning restrictions is a different question, which apparently wasn’t raised by the plaintiff. Under current law, the answer is probably that such preferential exemptions do not violate the Establishment Clause, see Cutter v. Wilkinson (2005).
Thanks to Prof. Howard Friedman (Religion Clause) for the pointer.