If you think separation of church and state exists, you should look at 90% of this election's Republican candidates, as well as the fact that churches don't pay taxes .
That being said, I'm not getting married in a church, obviously, since I'm atheist. But I do not think churches should be forced to marry gay couples if they don't want to. That couple can go find a more accepting church. They do exist; there's one a few towns over from me.