The equal protection clause is different from the due process clause, and Thomas can easily split his decision over that. As an originalist too, he would likely ask if the 14th amendment was meant to protect the rights of black people to at the time, and it was clearly meant to protect the rights of recently freed slaves so it isn’t much of a stretch, you can basically trip into this interpretation.

So I think he would be wholly unbothered making that distinction, knowing that _his_ rights are protected under a different clause. I guess it does show some of the fragility of judicial precedent, you could imagine an even more conservative justice who was not Thomas restricting the interpretation of this clause to mean only the narrow rights the majority of people in 1868 would have liked and not include miscegenation through some horribly tortured logic. But Thomas can draw the line before that and after himself.