I do love God and I love the Bible, and I work hard to believe what they say. But, it may surprise you, I don't necessarily think prayer in schools is a very important argument.
If you really trust the government, and you really believe the government knows what's best for you, and you really believe the government's laws won't be twisted and subverted, then yes, the government should allow prayer in its schools.
The bottom line is, prayer is a conversation with God, even if just in our thoughts. If I'm in a place that says I must pray, or must not pray, or I must pray this or that, as long as my prayer is my own, to myself, nothing can go wrong.
My fear is that when government starts talking too much about prayer, it will make one bad decision that leads to another and another, until people are forced to pray one specific way to one specific religion, excluding all other non-government regulated religions or deities (or however a politician might word it...)
If removing prayer from schools avoids a future like that, I'm all for it. As it is today, kids can pray quietly or silently any time of the day they want, which is fine with me.