it doesnt matter if you believe there should be a seperation of church and state or if its in the bill of rights in the 1st ammendment because it doesnt matter. The bill of rights doesn't directly apply to state governments (barron v. baltimore) and the post brown v board civil rights incorporation has only incorporated things like due process, miranda rights, right to counsel, free speech, no double jeopardy, some instances of eminent domain.
but marriage is not under the application of the bill of rights or any federal laws. it is a state power. We have granted the power to marry to the institution of the state. You have to have some form of government to regulate marriage as it affects housing, economics, tax benefits, as well as a major social regulatory power (the same as child abuse, sex predators, hand guns in school zones) and as the constitution states, every state must be republican or hold votes for certain laws.
since we are fundamentally a democracy, and the power to marry is a state power, then the vote should be the definitive factor in deciding local policy. If the majority of the constituents within a district dont want to live in a gay neighborhood, then they shouldn't have to.
Eventually most states will tolerate them, thats just simple social paradigm. But for now if people want to uphold the family and their term of marriage, then they should be able to and the government shouldnt infringe on their rights either, especially since they are afterall the majority.
I know it sounds like tyrranny of the majority but so is a near 60 seat majority in the senate, 3 justice appointments, and a radically leftist president.