I don't know if this reassures you at all, but I went to Catholic School from 5th - 12th grade and I seem to have turned out fairly non-traditional-religion friendly. I did go through a brief period of overattraction to the ritual and pageantry, but even during that time I retained a healthy skepticism.

It's kind of funny, I think about that time now -- while I didn't believe in God or a lot of how the Church said I should behave, I did really kind of throw myself into the rituals. My only lasting damage seems to be that I retain a love for the theatrical-religious stuff, a belief in ghosts (which is contrary to official RC dogma), and being mildly convinced that some kind of numinous presence exists somewhere in the universe.

Anyway, with reasonable counter-programming at home, Christian School probably won't hurt Ike even if he gets a little weird for a while.