Okay, I hate to do this, because of recent events, but, speaking as a "person of color", and one who has roots in the South, I could care less the "real" reasons for the Civil War. The fact of the matter is that the South, and in fact the United States for that matter, shouldn't have been engaged in the practice of slavery to begin with, especially given that the Declaration of Independence and the Bill of Rights (along with the US Constitution) was suppose to be documents sanctifying the rights of free men and democratic values. When talking about the justification for the Civil War, ultimately, there are victims involved: the men who actively fought the war, the destroyed lives (on both sides) as the result of the war, and the freed men women who, after so long, had to learn how to be citizens of a nation that may or may not be hostile to them. And because of this, I blame the gutless politicians who couldn't compromise on the issue of both slavery and states rights. But more to the point, I blamed the Founding Framers for the Civil War, for not having the foresight that a country built on the values of a democratic Republic will end up becoming a House Divided. Ergo, the roots of the Civil War can be found on the street corner of Cowardice and Convenience. And again, as a "minority", I could care less about the reasons for the Civil War, but I do care that my people were freed in the end.
I think societal change is rarely drastic and sweeping. I think it's more usually incremental.
The Founding Fathers had an idea of a country where "all men were created equal," but their idea of "all men" might not have included people of colour outside their own race. From their perspective of the time many of them might not have seen people of colour being included in the definition of "all men." It's wrong and they should have seen it differently, but apparently they didn't.
And politics is also the exercise of compromise and negotiation. It's possible some of the Founding Fathers believed people of colour should have been included from the start, but the reality of the times (the perspectives of the majority) might have precluded that from happening right then and there. They effectively deferred it to future generations to deal with.
This episode could have been done a number of other ways. I wonder how it could have played out if it had been McCoy and Uhura who had fallen prey to the nanites. And it didn't have to be a story dealing directly with Civil War era soldiers.
Which brings me to a story idea I believe had been floated way back during TOS dealing with a planet where blacks were the dominant race and whites were the slaves. Obviously they didn't have the nerve to deal with the issue in such a head-on way back then and the idea was softened somwehat through the episode "Let That Be Your Last battlefield." Then there's also the embarrassing TNG episode "Code Of Honor."
This does make me wonder if there are any stories TOS passed on that could be salvaged and adapted today by STC. Certainly NV/P2 have done that with stories originally slated for the aborted Phase II series.
I also agree with the comment upthread about the episode's running time. I, too, would prefer the stories to clock out closer to 50 minutes rather than the contemporary 42 minutes.