Are you questioning the outcome or the process?
If a statement that evolution is a theory and that there are problems with that theory amounts to "an establishment of religion" then whatever process there was that led to that conclusion is deeply flawed and needs to be fixed.
The constitution does not state that the Supreme Court will have the final say on whether or not some action or law is unconstitutional. When I see decisions like this one I question the wisdom of Marbury v. Madison. There needs to be a check and balance against the courts.