It's not somebody's civil right to be married in a particular church. Married yes. Having a particular church do it, no.
Well there's lots of bakeries around too, the couple in Oregon could have gone somewhere else, but the judge said that discriminating against them on the basis of sexual orientation was illegal, and whacked the bakery owners for something like $135,000.00. I'll have to go back and see if he was ruling under federal or state law.
Edited to add: The judgement in Oregon was under state law.