Well, DUH!
Because if a teacher leads the child in prayer, he is violating the clause that says that the government may not abet the establishment of religion.
Suppose the teacher is a Muslim: do you want him to teach your kids to grovel to Mecca with his butt in the air?
Any kid that wants to pray by himself has every right to do so, quietly and to himself. Prayers led by adults or other children and condoned by the school should not be allowed.