A lot of people here have gone to religious schools and are now atheists. That says to me that the school can only "brainwash" a person so much.
Our kids grow up, they do learn to think for themselves.
My kids go to a catholic school, and the reason I like it is because it is a small school and I was really worried about my dd when she first started because she was so shy around kids.
Honestly I don't pay attention to what she learns in religious studies but so far from what I see there's lots of focus on loving, respecting, appreciating friends and family.
I am not suggesting public schools don't do the same.