As far as the Scouts being able to have meetings in the school, the US Supreme Court just had a school-church case and ruled that "the Free Exercise Clause protects against “indirect coercion or penalties on the free exercise of religion, not just outright prohibitions.”

"But the exclusion of Trinity Lutheran from a public benefit for which it is otherwise qualified, solely because it is a church, is odious to our Constitution all the same, and cannot stand."

You would have the government (the school district)  deny the Scouts because they have a Deist requirement. 

That is religious prejudice and discrimination.  To reiterate:  "the Free Exercise Clause protects against “indirect coercion or penalties on the free exercise of religion, not just outright prohibitions.”

Don't feel bad, we agnostics don't get to penalize anyone else for their beliefs, either.

Both of us together are only 7.1% of the US population; the First Amendment is not going to go away!