Their fear was not that references to religion would be made in public education - a system which had not yet been unconstitutionally foisted upon the public -- but in regard to the establishment of a specific denomination or church body as the official religious body of the United States.
The Dover school boards actions are so far removed from what Hamilton and Madison were discussing as the distance between galaxys.
Your interpretation of the "separation of church and state" would ultimately prohibit anyone who believed in God from holding public office or even voting.
Balderdash. I was asked about arguments pertaining to separation of church and state, and lo, there they are. Whether that applies to public school curriculum, I recommend you take up with the implementers of the post-civil war amendments, and the taxing authorities who tap our wallets to pay for public education.
This rather strikes me as a hard sell, since the constitution authorizes a rather broad mandate for securing the orderly business of the people, in and around the Commerce Clause.