Many churches do, and it is not illegal yet. But you miss the point, the churches are owned by the believers. The public schools are owned by the public and not by the courts or by barking moonbats. It is school boards and local taxpayers/parents who should make decisions.
For proof of this argument, I highly recommend reading in today's WSJ the review of Christine Rosen's book "My Fundamentalist Education". This woman was taught that the world was created in 6 24 hour days, and that all the dinosaurs drowned in the Great Flood. Yet, she survived, and wrote a book about it.