I haven't read his opinion, but from the paragraph quoted, I'd guess he's not conflating state and federal, he's comparing judicial to legislative branches, and saying it'd be better for gay marriage to win legitimacy in the legislatures and populace, not be imposed by the courts.

Obama's favorite legal scholar, Cass Sunstein, is a judicial minimalist with similar views, I'm told. I think the warning example would be Roe vs. Wade, still fought heavily because abortion rights are pretty unpopular.

People talk about the courts protecting minorities from a majority, but if the majority really has it in, that won't work well. Arguably the courts work best when they clear away legal cruft that the majority hasn't gotten around to yet -- which given the rapid change in public opinion on gay marriage, seems to actually apply here.