Uh, first of all, marriage laws clearly do not amount to an "establishment of religion" within the meaning of the First Amendment.
Agreed. Considering that the establishment applies to the states by virtue of the Fourteenth Amendment, M&C's position would imply that all marriages are unconstitutional. Needless to say, nothing of the sort was intended, meant, or enacted.
Furthermore, as A18 suggests, a constitutional amendment supersedes any previous provision to the contrary. The only forbidden type of constitutional amendment is one that deprives a state of equal representation in the Senate without its consent.