The freedom to marry doesn't mean it has to be done in a church. I'm sure there are many churches that would never allow a gay couple to wed in their halls. On the other hand, I'm sure there are some out there that would allow it. It depends on who is running the particular church, but I believe that's something that should be decided by those running the church, not the government.
As far as people being encouraged to be gay, I doubt that's going to be an issue. People are going to be who they are; it's a matter of feeling comfortable enough to come out, rather than try to hide one's identity for fear of backlash from others, an ordeal I understand all too well.
I still haven't told my mother I'm bigender; she's not the tolerant type when it comes to LGBT individuals.