Here's another way to look at it:
The 1st Amendment provides for the free exercise of religion and the 14th provides for equal protection under the law.
So, a Christian students gives a prayer over the PA system. Does a Muslim student get the same opportunity? No? Then you have violated that Muslim student's free exercise of religion as guaranteed by the equal protection clause of the 14th Amendment. A Jewish student wants to give a prayer? A Hindu student wants to give a prayer? A Buddhist student? A Zoroastrian student? A Rastafarian student? A Pastafarian student? etc...
If one religion is accommodated in the public school, then all must be. What we end up with is making a mockery of all the religions.
Too much time on a Submarine?