I'm not sure you'll like the first comment, but I think you'll appreciate the second one.
On the choice of school:
* If her dad didn't care enough to fight the issue, I would drop it. This is part of the strategy that allows me to keep my sanity. When I say "drop it", I mean "let it go". He obviously doesn't think it's big enough of an issue to argue, and he is the parent. Can I be friends with people that are of different religious beliefs? The I can certainly accept the fact that my DSD is choosing something that I don't believe in. It's even easier when she is 5 and it's just a school. It's as simple as that.
On gay marriage:
* In this very house we have many conversations about it. The very first time DSD confidently mentioned something about "only man and a woman should marry", I remember standing in the kitchen and taking a breath to compose myself. She was about 11-12 at the moment, and her stepdad has rather intolerant outlook on the issue. I remember saying something like, "Well, I believe that love matters more than anything else, and that I am in no position to judge whom other people choose to love. Better than hate any day." That was it. The rest came from small comments and conversations like that, and now that she is 16 she is not only friends with many gay kids at school, but she also called here one time in tears, because she got into a heated argument with her stepdad over this very topic, and she said she did it because she didn't want to have her little brother and sister growing up with intolerant views. A very proud moment of mine.
The point is... Believe it or not, I am Christian Orthodox, that goes to Catholic Church with her boyfriend, has half family that is Jewish, believes that gay people should have the same rights as the rest, lives "in sin" with her beloved for 6(?!) years now, and is still hoping for salvation.
What I'm trying to say is that catholic school is not going to overpower what you present at home. And if you set an example of love and tolerance, your children will follow. Being in a blended situation, you are going to allow yourself to let go of some of your beliefs and to allow her mother imprint some of hers. That's just what's going to happen, and it is important to allow everyone to have a say, and the child will choose what she is drawn to at the moment, . Don't stress.
P.S. I really do think that the next generation will be way more tolerant than the past.
P.P.S. it is important to remember that it will take years until she actually settles in her opinions on such questions. DSD's view of the world (including right and wrong, marriage, relationships, parenting, etc.) is NOTHING like when she was 6 y.o., it's not even close to what it was at 12. Go figure.