This is the real reason for this ruling. Muslim prayer is not silent. If the legislature voted to allow muslim prayers to be broadcast over the intercom at the appropriate times, the court would probably approve it.
My kids go to a public high school that is highly populated my muslim kids, and they let them out of class on Fridays to pray in the hallways if they want or to leave and go to their mosque. I guess that ACLU guy is right—kids can pray anytime during the school day they want to.