I've never run into these sort of problems. And there are a few reasons for that.
First, I run D&D alignments according to what I feel is the clearest definition, those given in the 1E DMG. There, it defines good as respect for "human" rights, of which there are three that are enumerated. Human in quotes, of course, because this will likely extend to other races in a D&D world. But exactly where the line is drawn is left to the individual DM.
Evil is not defined as the mirror image of good, however. For evil, purpose is determinant. It takes priority above and beyond the "human" rights, and so evil is willing to trod on human rights for the sake of their "greater purpose." There is no requirement that evil's purpose involves mustache twirling. The purpose could be a seemingly noble one.
What this sets up is a system where you can clearly and objectively know whether an act fits in with good or evil. But at the same time, by being sufficiently broad that evil can have a noble purpose, you can have a moral ambiguity vibe to the game.
As for historical morality, the differences really are over-stated. Or maybe just wrongly stated. Natural Law did not start with Thomas Aquinas. It has its roots in ancient philosophers, and you see bits and pieces of it emerge throughout history. A lot of ancient and persistent ideas began being put into modern form with the School of Salamanca as early as 1177.
Regarding slavery, there were old manuals written for slave owners describing how you had to break the will of slaves, revealing that it was always understood that slaves were human beings with self-determination, and keeping slaves meant destroying that. This is not a modern insight. To most modern eyes, you look at Mark Twain. White dude who lived in the antebellum south. Wore a white colonel suit. He clearly must have loved slavery. But I can't help but think he was being subversive in his writing when N-word Jim has hopes and dreams. Property doesn't have hopes and dreams. I would point to this as yet another indication that the culture understood the gravity of what slavery meant. There were just political reasons to ignore clear and present reality. I would think the political climate of the present day makes it clear just how easily that can happen.