Derb, I think you are right to say that the nature of the case required Judge Jones to make a determination about the definition of science; in suggesting that it is unwise for federal judges to do such things, I meant to criticize the jurisprudence the judge was applying rather than the judge himself.
As for parents who have a grievance about what their local school boards are doing to their kids’ education, they can throw the bums out in the next election–as they did–without going to the federal courts. (Ideally, they could also use tuition tax credits to send their kids to private schools more to their liking, but I may be going back to libertarian neverland by raising this point.)
If a parent did go to federal court complaining that his school was teaching alchemy in its chemistry courses, I should think the proper response of the judge would be: This seems like a gross dereliction of duty on the school’s part; I am terribly sorry that your neighbors and you are being subjected to such foolishness; but you have no federal constitutional claim for redress from me. And something like that would be the answer that the courts would actually give in such a case.