In my opinion, the Religious Freedom Restoration Act of 1993 (RFRA) is a “law respecting an establishment of religion” that violates the First Amendment to the Constitution.If the historic landmark on the hill in Boerne happened to be a museum or an art gallery owned by an atheist, it would not be eligible for an exemption from the city ordinances that forbid an enlargement of the structure. Because the landmark is owned by the Catholic Church, it is claimed that RFRA gives its owner a federal statutory entitlement to an exemption from a generally applicable, neutral civil law. Whether the Church would actually prevail under the statute or not, the statute has provided the Church with a legal weapon that no atheist or agnostic can obtain. This governmental preference for religion, as opposed to irreligion, is forbidden by the First Amendment. Wallace v. Jaffree, 472 U.S. 38, 52-55 (1985).
The unconstitutionality of RFRA has also been a theme of Marci Hamilton’s work; she also submitted an amicus brief in the Hobby Lobby case arguing that RFRA was unconstitutional. She has four theories: (1) RFRA violates the separation of powers, (2) RFRA violates Article V, (3) RFRA isn’t justified by any of Congress’s powers, and (4) RFRA violates the Establishment Clause. I disagree with (1) through (3), but am sympathetic to (4). In any event, you can read her brief here.
Note that there may be strong originalist arguments that religious exemptions were permissible at the Founding, so I’m not trying to make any strong originalist point here — just that, as a first-principles matter, I’m not wild about the idea of religious exemptions, and find them to be in strong tension with my Establishment Clause sympathies.
Note also that if I’m right, the solution isn’t necessarily to invalidate RFRA. It could be to extend RFRA to apply to deeply held secular convictions, as Justice Harlan suggested in his concurrence in the result in Welsh v. United States (1970). See also section I.G of Eugene’s article, A Common-Law Model for Religious Exemptions, 46 UCLA L. Rev. 1465 (1999), which discusses how draft law has been interpreted this way, as has Title VII’s religious accommodation requirement.