The Bill of Rights originally applied only to Federally enacted laws. After the 14th Amendment, however, the Supreme Court has consistently held that most of the rights found in the Bill of Rights are incorporated by the Due Process clause. (Under the Slaughterhouse cases [1871], there are very few Federal privileges and immunities.)
My humble reading of the First is that it is a specific limitation on what the Congress is allowed to do. I would not interpret it as granting rights to the people, per se. The second amendment is a right of the people, and many other parts of the BOR, but the First is a restriction upon the Congress.
In any event, the addition of the term "separation of church and state" into conlaw that began 50 or so years ago is totally bogus in an "original intent" view. I think it's safe to assume that the political class that went to the trouble of writing and ratifying amendments would have seen fit to enforce them afterward. So the manner in which they were enforced in the years immediately after their ratification should be judged as reflecting the true intent of the writers.
A Constitution that can be interpreted differently than it's writers intended is meaningless. They shouldn't have even bothered to write it down.
I'm glad how this case turned out because I think that evolution is solid and should be taught. But I wish that we would return to the idea that the constitution means what it says, and if we don't like what it says then we should amend it.