OK.
I'm not sure I agree with his parenting choice. Fine, you want your kid to make up his own mind about religion and spirituality and so forth. But if that's what you want, don't enroll him in a religious school at such a young age. Kids are easily influenced at that age and the stuff sticks with them. Then, 15 years later, you're going to get a kid who believes in faith over rationality, scripture over science. FUCK THAT.
Enroll him in a normal, secular school and let him make his choices.