A store can say "no shoes no shirt no service"
Churches should be allowed to do the same without losing government funding. I'm all for gay marraige, but forcing an institution to participate in something that's explicitly against their beliefs is fine. Besides that, gay couples will probably face discrimination (no matter how uncalled for it is) if they're married in a Christian/Catholic setting. And imposing punishment in the form of reduced funding is severely crippling, especially since churches run solely off of donations, fundraisers, and said government money.