Exactly. I'm a Christian too, Roman Catholic in fact, and am one of the biggest EVA fans there is, especially a fan of it's multi-faceted use of religious icons, symbols, and references.
I personally take no offense to it because I realize three things:
1.) Its just science fiction, and on top of that its an anime.
2.) They are mere references to said religious items, and don't use them or refer to them in such a way that it would be completely blashemous to God, a god, gods, deities, etc.
3.) As long as a christian, jewish, greek, etc. viewer is strong enough in their faith, and educated enough in their respective religion, then they will know better and be confident enough to not care, since they know how it really is.
As for non-christians or non-religious, I doubt they would take an anime seriously, even if they don't know enough about the religious references. And being that they probably don't, theres no harm in them seeing it because they won't understand what going on, on the level we do.
In a way, you almost have to be religiously knowledgeable, historically knowledgeable, to know what the hell is going on in Evangelion besides what the obviousness of whats going on on the surface.
