I agree that the notion of compromising political, civil and human rights, especially of minority persons and communities, ought to make us very uncomfortable. I think with respect to GLBTQ persons, same-sex marriage, and related issues, the following principles should be honored:
1. No-one who disapproves of same same-sex marriage should be required to enter into one.
2. No-one should be required to accept an invitation to attend a same sex wedding, or any other wedding.
3. No minister should be required to officiate at a marriage that does not comport with the requirements of her or his faith community.
4. There must be no discrimination against GLBTQ persons in accessing services of government or business.
A related issue: it’s probably time for ministers to cease functioning as agents of the state when they witness marriages. 
The US Bishops have done a pretty thorough job of trashing the notion of religious liberty. It’s time to just stop.