A church is a sacred place and should be respected, as should a synagogue, mosque or temple, even if you do not share the religious beliefs of others.
I did it once because it is kind of a taboo, and I didn't think I would get caught. I can't think of a reason to do it a second time.
I wouldn't have a problem with it. I see no reason why our creator would be upset at two humans making love in His house. Having said that, I wouldn't want to do it in any way that would be considered disrespectful, such as doing it on the alter, or in front of others in the church. As I mentioned in another thread, I used to fantasize often in church. But having sex there would be a first.