Well, as a rule, yes, they should have autonomy. But here we're talking about a government school's clear attempt to get students to believe that one or more gods living in some supernatural realm govern what happens to us in this world. It's a clear violation of the 1st Amendment.
When they actually start invoking the Book of Genesis to back up their theory, then you'd have at least the beginnings of a case to make. Until then, it's just theory that you disagree with. I think the people are capable of deciding that in their own school districts, and especially in a situation, there will be plenty of debate and plenty of opportunity to persuade the voters. That's how things are supposed to work in a free republic. It's sad that so many people around here don't get that.