The question of agency, morality, and representations thereof in games is an interesting one, but I don't think the answer is as cut and dry as you're suggesting. Have you played many wargames? AHD is a light strategic-level wargame, great for an introduction to the genre. However, wargames generally don't make explicit judgments on the belligerents portrayed because the focus is on the military strategy and tactics rather than the surrounding politics (To answer your WW2 question - I haven't played a WW2 -wargame- that depicts Nazis as evil, only ones that depict Nazis as soldiers. Not even Memoir '44, the most likely WW2 wargame to be played by non-grognards, does this). If what you're looking for -- and this is fine -- is a section in the rulebook that says "by the way guys, you're about to suit up for the grays, so remember: slavery was wrong", you probably shouldn't look at wargames as this type of game is about military history.
For further "reading", a good game that takes a focused look at slavery is Freedom: The Underground Railroad. This one is a co-op game, so you aren't even given the option to play as an anti-abolitionist -- this is a conscious moral stance taken by the game designer that you may appreciate. Another game you may find interesting in its design is Here I Stand, which is a wargame that attempts to model not only strategic military operations during the Wars of Reformation, but also the political, diplomatic, and even religious influences on what conflicts were even being fought. My last suggestion for you to look at is Labyrinth: The War on Terror - this game takes a particular tack in representing the US and Jihadi factions by speaking from their respective viewpoints rather than using the players as outside observers.
Oh, and Brenda Romero's game Train, of course.
Lastly, I take issue with your statement that "to not acknowledge those truths is to allow them to be questioned". The moral and ethical arguments against genocide, slavery, rape, etc. are very strong and well-trod. Stopping discussion doesn't stop opinions from forming, but it does stop the scrutiny of those opinions, which in this particular case is an opinion that is extremely easy to debunk. In other words, someone who thinks that e.g. the United States should return to antebellum slavery is probably not going to be swayed back by anti-slavery rhetoric in A House Divided -- this rhetoric is taught in elementary schools when covering the ACW, and reinforced through every level of education. This isn't to say that games can't or shouldn't take sides (games with opinions are some of my favorites even if I don't always agree with those opinions -- see the games of Phil Eklund for example), but to say that games do exist within the context of our society at large and that taking the purpose of a game into account informs how the design treats the subject matter.