A school system should be a part of the community meaning that the tax payers and parents of the district should be the ones to decide what does and does not occur in a school and how their students are treated; but school is also a place that should create equality for all students. It would be much more logical to ignore religion altogether in schools than to force it upon students who may have different beliefs.
I think that people should have the ability to pray if they feel they should. In terms of what the schools may think that may be a matter best left with their parents instead of the school or it's administrators. This seems to be something that the schools may stay out of the way.