I went to a public high school that did not allow students off campus during the school day. Parents knew where their kids would be during the school day. Parents had a measure of control over the school system - the admin is responsive when parents get involved. Had my school allowed kids to leave during lunch, there would have been a lot more problems with drugs (and kids making really poor choices).
My comment was not specific to the circumstances of the "Jesus lunch". I don't care about that one way or another. If parents are bitching about it to the administration, you are going to get a response like what is described in the OP. The situation is entirely avoidable by keeping the kids on campus. This isn't a liberty issue IMO. Local issue is local.