Assuming atheism, I see no good argument against miscegenation laws. Jefferson said that we were endowed by our creator with certain inalienable rights, and if we have no creator, then there are no inalienable rights. A right exists just in case there is a moral fact that requiring those with the biggest guns from exercise power over those lacking the biggest guns. However, if atheism, (or at least materialistic atheism) is true, then there are no such moral facts, and there is no obligation on the people with the biggest guns from disallowing mixed marriages if they so prefer. Thus, if the government under Trump wants to make America great again by making America white again, and part of that operation is to prevent mixed marriages in order to maintain racial purity, there is no moral fact that obligates them not to do so. Similarly if the people with the biggest guns like gay people then they will give them marriage licenses, and if not then not.
On the other hand, if there is a God, then God may have revealed to us the basis of the doctrine of human equality, then that is another matter. The concept of race has no basis in Scripture, and there is no religious reason at least in the Judeo-Christian tradition for treating people of different races differently and preventing intermarriage. The only ethnic identity God seems to care about in the Bible is the lineage of Israel, and the lineage of David, and in Judaism and Christianity that is best defined in terms of a special mission, not a special privilege. There was concern about intermarriage for fear of the Jewish people falling into idolatry, but that is not an issue for miscegenation.
On the other hand, in that context, we have to ask whether God intends for same-sex couples to marry.