You're missing the point. Permission slip is not the issue. The school said one thing and then did something different. There was no mention of indoctrination or prayer. That's why the school apologized. You don't apologize unless you did something wrong.
You have a misperception. The school is not the boss. The parents are. That may be hard to comprehend for a statist like you.
You have two misperceptions you need to clear up.
One, the school is in charge. If you don't like it, then you remove your child.
Two, I think what you are calling "indoctrination or prayer" was cultural exchange, and I believe someone among the parents or opponents or the program are lying.
The school took the easy way out, and that was wrong. The principal and superintendent should have called an open meeting with the media there with the families and explained exactly what happened.
That is how life in public is handled. You, Jack Fate, are not an island to yourself.