Well as someone who is not religious, I say let those who HAVE to pray, pray. For instance Christians do not NEED to pray in the middle of the school day, certain other religions might require them to do so.
Prayer in schools is not banned anywhere in this country, what this is referring to is a supreme court case in the 60's preventing teachers from leading prayer at the start of the day, this is the only thing that was ever in question. So the debate is off course, the question has actually been, should teachers lead the class in prayer in public schools?
There are christian clubs and student lead prayer groups before the school day all over the country, and this is just freedom of religion and not in my mind worth debating the merits of.
It's "Freedom of Religion" and "Freedom of Assembly," it should definitely be Allowed. It's their right to do so.
That's all I got to say, it's their rights.
I say if you want to say a quick prayer, then do it, silently. In your head. I think that with freedom of religion, as long as you aren't flaunting it then you should be allowed to pray. And as long as you aren't forcing others to believe what you believe, then it should be okay.