The 1st amendment protects free religious practice (minus what has been defined by the courts over the years as not under the 1st amendment). If I make up a religion that rejects everything- perhaps in the shadow of the original Greek Skeptics, then I become unfailable under your system.
Sorry, but I don't care if you choose to brainwash your kids. School is about learning and kids should be taught about the real world. Now when they go home and what their parents tell them there is a whole other story- the parents can (foolishly) just say don't buy that malarkey if they really want to, but the kid needs to still understand what evolution is.
regardless, the school has no right to discriminate against someone based on religion.