The purpose of school is to learn.
The school's responsibility is to provide a learning environment in which every student can feel comfortable, and every student is equal.
The minute you start a prayer minute, or group prayers that equality, and that comfortable learning environment is lost.
Even if the school does not sponsor the prayer, even if 15 of 20 kids decide they are going to pray, I believe it is the schools responsibility to say, please refrain from prayer sessions during class. That way the rights of the other 5 kids are protected.