I never got into dealing with the topic, because A) I don't think pulp adventure stories are the most appropriate platform to discuss heavy real-world atrocities, and B) it never figured into the written adventure paths.  I always used the Confederates as an easy-to-hate villain faction and let the players decide how much they wanted to fill in the blanks.  Like how comics and games and movies have used the Nazis as easy villains for decades without needing to bring up the Holocaust every single time.