The prohibition of school prayer is consistent with religious liberty. The prohibition is that no school official may lead students in prayer. This does not mean that students cannot pray on their own silently or even aloud. The prohibition is important because of the separation between church and state. It also allows more religious freedom because students of all religions (or no religion at all) attend public schools.
No, the prohibition of school prayer in school is not consistent with religious liberty, because it prevents students who want to pray from doing so. If 90 percent of the students in the school wanted to eat potatoes every day, the school would offer potatoes for those who wanted it. The vast majority of Americans are still Christian, and should be allowed to pray if they want to.
We should not prohibit prayer in schools as it not only prohibits entire classes from praying together but individual students. The first amendment to the US Constitution (Our second right to exist, the 2nd amendment was the first) states that all people in the United States have freedom to believe what they wish to believe. School is no exception.