Now, "no" and "virtually no" are not quite the same thing. "No intelligent reason" would mean that there is, well, no intelligent reason. "Virtually no intelligent reason" would mean that there is intelligent reason, just not very many. So which is, Justice Scalia? No reason, or some reason, to discriminate on the basis of their skin? The difference between "No" and "Some," between X and not-X, is not inconsequential.
Scalia is right about one thing: at stake here is precisely reason. If we think about Lonergan's four-fold imperative--Be Attentive, Be Intelligent, Be Reasonable, Be Responsible--it goes without saying that sexual and racial discrimination are irresponsible, and thus it is quite appropriate to frame the matters in a moral dimension. But they are irresponsible precisely because they are unreasonable. If we lived in a world wherein women and men really did have vastly different capabilities, such that either was genuinely incapable of performing certain tasks, then things might be different; likewise what skin colour. But of course we do not live in such a world. Of course I'm not talking about basic realities surrounding the reproductive process: at this point only men are capable of fathering a child and women of bearing one to term. Policies designed to take these realities into account--such as paid and protected maternity leave, although of course paid and protected paternity leave is also a good thing--are not discriminatory but simply aim to take into account that reproduction is generally speaking a physically more taxing process for women than men. Such policies can be quite responsible, precisely because they are grounded in reason. They are a world away from barring women from certain professions or shooting unarmed teenagers simply because they have relatively high levels of melanin in their skin.
Fundamentally the problem is that Scalia is not speaking from a commitment to reason. Rather he's speaking from a commitment to ideology, which Lonergan defines as the effort to justify a recurrent failure to be attentive, intelligent, reasonable, or responsible. There is a simple test to see if we're dealing with ideology or reason. Ask Scalia whether there is reason to discriminate against persons of Italian descent. See the response. One suspects that the answer will be no reason, not virtually no reason. And he'd be right, but it'd lead to the question why is there is only virtually no reason to discriminate against persons of African descent.