I see what you’re saying, though I don’t agree completely. An “unpopular group” has in fact been a term used by the Court. See this sentence from Windsor:
The thing about practitioners of bestiality is that they’re not really a “group” in any recognizable way; they’re just people who happen to all have some desire or practice in common. For this reason I don’t think the Court would take seriously their complaints of being discriminated against. Gays, by contrast, have everyone treating them as if they’re a full-fledged race. (Toeiva advocates can barely talk about their issues without invoking race metaphors.) This doesn’t make sense — it’s just how it is. They see themselves as a social group and so does the law.
It’s in Kagan’s interest (as a member of the hard left of the Court) to spin this case as primarily being about moral disapproval, because that’s a broader concept than animus and it increases the likelihood that Windsor will be used as a precedent to impose toieva marriage everywhere.
Windsor does use the term disapproval (once). But Windsor says a lot more than moral disapproval — it also mentions animus, bare desire to harm, etc. Even if there is some great unexplained significance to the term disapproval, it doesn’t mean that any laws based on moral disapproval are invalid. Rather, it would mean that laws based on moral disapproval that are meant solely to harm the disapproved-of group call for heightened scrutiny or are invalid.
The funny thing is that the Court’s decision does not say whether it is applying rational-basis or heightened scrutiny, while Scalia’s dissent seems to argue that the majority either employed rational-basis review or was a substantial-due-process case in disguise, and Alito’s dissent says the Court used some kind of heightened scrutiny. Confusing indeed. I believe Kennedy is known for his confusing opinions — this case will certainly support that aspect of his reputation.