I haven't fought this fight, but I've thought about fighting a similar fight in that my kids' public school does projects that look to me a lot like Christmas projects. I wouldn't mind that if they included other traditions, but they only do the secular US Christmas junk.
Here are my thoughts as a practicing Christian whose children go to a public school:
1. The constitution clearly protects separation of church and state. There is no state-sanctioned religion. This, I believe, is one of the great strengths of our country, and I'll go to great lengths to defend it.
2. The school, as a governmental agency, is not to sanction any one religion or belief system. Since prayer is automatically to a 'higher power', school-sanctioned prayer automatically excludes atheists. The school need not deny the existence of religion. Indeed, I'd be thrilled if the school gave a balanced overview of all the world's religions and belief systems.
3. As a society, we have an obligation to protect minorities, especially minorities with whom we disagree. Freedom of speech doesn't just apply to people who say things I like. Religious minorities are the hardest to 'see' because no one can tell from the outside that you don't believe what everyone else does. Thus, schools should err on the side of caution when religion comes into play. They should avoid school-sanctioned prayer and even the appearance of school-sanctioned prayer.
4. As a society, we have an obligation to protect children. Children, unlike adults, are less able to stand up for their beliefs, especially if they're different from the 'norm'. It's very easy for children (even teens, or maybe especially teens) to be coerced into doing something they don't want to do so they won't stand out. The people in power in schools should not put children in a position where they're made to feel 'othered' and required to defend their beliefs, because they are going to be less able to stand up for their beliefs in the face of the power of the teachers/school structure. Thus, nothing in the structure of school or school activities should include prayer.
What this means for me is that schools should not have any adult-led prayer in schools ever. Student-led prayer can't be forbidden, but it certainly can be set up so that it's not focal. Band leaders, for example, should not lead prayer (even if they're students) because again the issue of power and coercion. If there is student-led prayer then there should be something equal for the other children to do for community building. Students of all beliefs should be made aware of the constitution and the case law surrounding this issue.
Finally, as a liberal Christian, I would say that I don't WANT someone else teaching my kids to pray. The beliefs of people who feel compelled to pray in public are usually considerably more conservative than what I believe. I don't want my kids to have their baggage. It's my job to teach my children our religion.