This concern is not really about gay marriage, as others have noted. It's about whether those who are opposed to homosexuality itself on the basis of their religious beliefs have a right to discriminate against gay people in the public sphere. Even Rod agrees, confirming that this concern is not about whether churches have to marry gay couples or whether priests can get in trouble for anti-gay sermons.
Sorry, folks, but this issue is settled. Romer v. Evans has been the law for 13 years now. This sort of discrimination is not allowed.