If we are going to separate "Church and State" entirely...it should be across the board. No exceptions.
What does that mean, exactly though?
It means freedom of religion and
freedom from religion.
It means you can't be forced to participate in anything, but that people are free to participate as they wish and need to, when they wish and need to, and pretty much
where they wish and need to.
It also means that such participation shouldn't be disruptive-in the case of the Muslim obligation to pray, they should be permitted to excuse themselves from class and go someplace quiet to make their obligation-the library, perhaps, or outside when the weather permits.
I don't see any conflict at all between permitting a person to practice their religious obligations, and not mandating a specific religious requirement, which is what the "moment of silence" was. There was a time when many U.S. public schools began the day with a prayer or Bible reading, and it wasn't clearly decided until the early sixties that school-sponsored prayer was
state sponsored prayer, and therefore, unconstitutional. This was the advent of the "moment of silence," and it was and is an attempt to begin the day with prayer, or at least a state-sponsored moment of acknowledgement. Again, not neccessary-while I
did pray during the moment of silence, I also prayed at lunch, and a few other times-no one knew, and I certainly didn't need to be provided a special time to share with everyone else......