You kind of have it backwards
Same sex marriage is covered under the 14th amendment to the Constitution
The judge is required by the Constitution to separate church and state
No not really, same sex marriage had the 14th applied to it, the 14th does not specifically cover gay marriage. The first thing the courts had to do was to make the decision that same sex marriage was equal to hetero marriage. ( this ruling has implications far greater than just marriage by the way)
As far as the judge goes, the state is dictating his religion and stopping him from following it. That is specifically prohibited in the constitution.
Either way, someone is going to have their rights put aside in order to accomadate gay marriage.
and like I said, how long before churches are forced to comply? as far as how does gay marriage affect you, this is a good example.
At any rate, Its against my religion according to those in charge, however I would personally perform the marriage and be happy to do it for them.
but that is my personal choice.