Well, first off, a lot of people misunderstand a churches tax exempt status. It isn't any different than any other non-profit, including gay rights groups!
Beyond that, no, I don't think a Church should be forced to marry someone they don't think they should marry. Even if I disagree with their choice. You may disagree with me on that, and that's perfectly okay. But that's the way I feel. I question though, why a gay person would want to get married in a church that was only doing it because the government told them they had to? There are tens of thousands of churches in the US of A that support and affirm gay marriage, there's a courthouse in every county, the Gay community does not need those conservative churches, why should we complicate the issue by enforcing gay marriage when they aren't even enforcing heterosexual marriage? (A church can refuse to marry someone because of prior divorce, or just about any other reason if that's what they think is right)