It may sound harsh to many, but I feel that there should be a separation of religion and school.
It shouldn't be an issue really. But I may be biased. I wasn't raised with God in my household. I think I said grace and then would listen to Darwin's theory of evolution. Also, it doesn't help that I am one of the few Jews in my very homogeneous school. There are two groups here. W.A.S.P's and Catholics. I am one of two Jews in school. And I feel it would be inappropriate for a educational facility in the United States to have prayer. Why should I pray? To whom should I pray? I don't believe Jesus is the messiah anymore than I believe God is.
Also, there are religious schools.If you want a more "wholesome" religious education, go to a religious school. Every denomination has a school. Keep God in church or in a religious school. But I feel it is wrong to allow prayer in a secular school. This is my opinion anyways, you are entitled to yours.