Scalia's argument isn't that marriage equality is an issue for the states. It that it's an issue for the
legislature; that is, that the
people should decide on it, rather than an interpretation of our secular scripture.
It's helpful to remember that the balance of powers were carefully designed, with an overarching purpose of not centralizing power into a monarchy or aristocracy. We are by design not a nation governed by a panel of philosopher-kings.
Because the Supreme Court has lifetime tenure --- a design feature intended to isolate the justices from politics, not embed them in it --- there's a lot of tension involved in their powers. Unlike politicians, they can't easily be removed if there's a popular outcry against their decisions. They're the guardians of the Constitution. But the Constitution is first and foremost a document of procedural safeguards: it is most coherently and powerfully understood as a mechanism to ensure that all citizens have open channels to the decision-making of their own governance. The procedures of US government are meant to be zealously protected, but the substance is supposed to be left to the people.
So a lot of the dissent in today's result is best read as, "regardless of what we think of marriage equality, who are we to override the decisions of the people?" And further militating against today's substantive intervention by five pro-equality justices is the fact that marriage equality isn't really a process right. Whether or not your marriage is recognized has actually not much bearing on whether you're capable of making your voice heard.
Of course, there are even more powerful arguments in favor of marriage equality. For one thing, the black letter language of the Constitution, right smack in the beginning of it prior to any amendments, requires all the states to honor each other's judicial proceedings, public acts, and records. To allow Mississippi to reject a Massachusetts same-sex marriage is to contravene the process set up in the Constitution directly. That can happen, but probably not when the conflict is animated entirely by discrimination against a class of people.
All this is just to say: don't be too quick to discard the intellectual argument against Supreme Court-enforced marriage equality. There will be times in your life where the same arguments are going to make a lot more sense, applied to other issues.