I saw it a few days ago. I liked it. My family and I were going to go see it on X-mas day, but my mom decided she didn't feel comfortable with it(Xtain and all). So we saw National Treasure 2.
Anyway, I liked the GC. It was a good movie, with interesting special effects and interesting story line.
I didn't see it as being against the church, unless your associate the Magisterium(Bad Guys) with the catholic church. Other than that it's not against Xtainanity.
It's about finding out the truth about the universe and the evil Magisterium will kill anyone who refuses to live the way they say everyone should live, meanwhile they are planning on taking this knowledge and forcibly making all of the other universes believing the same way they do. In that aspect, it's just like the Catholic church on their dealing with any new culture in the mid 1600's and so on.
I don't care if it is about a tongue in cheek reference to a religion. The movie is a good story about standing up for yourself and others that you love. Don't let any organization try to kill the ones you love and if you can destroy the evil organization(Magisterium) then more power to you.