I don't expect her to be treated different. In fact, I would advocate for equality. However, I do believe that exceptions should be made for religious observations/obligations for all. If a Muslim cheerleader needed to miss part or all of a practice I would not want her/him penalized for it.
Because its a public school, should separation of church and state impose school requirements before God?
Wow that is so far from what seperation of church and state is. Seperation means that the government is not allowed to make you practice a certain religion and they cannot ban you from practicing what you believe in.
I am a cheerleading coach and all of my parents and girls have to sign a contract as well. The purpose of it is so that everyone knows the time commitment and the cost and cannot say they didn't know. Cheerleading can be a sport. When one person misses it effects everyone. I personally will allow my girls to miss certain things without consequence depending on what activity they miss. Family commitments outside of school activities will never be subject to disipline as long as I have been informed of the days they will miss.
My advice is that if it is such a big deal to you that she has to miss a game then maybe she should not be a cheerleader or in anything else that involves a time commitment for that matter.
Have you ever tried to flip the senario if she missed the religion class they will not allow her to participate in the event either. It is a matter of what you would prefer her to miss. Why do you not accuse the church of discrimination like you are of the cheerleading coach? It is the same thing you know.