But you aren't tackling them head on, you are, quite literally, playing with them. Civ may use the backdrop of history, but it most certainly is not history. And you are suggesting to add in some of the "unfortunate" (understatement of the century) parts as tools to manipulated and played with. Asking questions like "How do I min/max the chopping of forests" is one thing, but "How do I min/max the ethnic cleansing of a group of people" is something else entirely. Further, while leaving them out may make a few players annoyed since the game is not "fully historically accurate" (a goal never set out by the game itself), to add them in could make those who were/are impacted by those things extraordinarily hurt by treating them as simply strategic tools.
Their inclusion adds nothing for gameplay/strategy that can't be added via other means, and is thematically questionable, by allowing people to recreate some of the worst parts of the human experience "for fun".
That's what I meant "we shouldn't add them blindly and without nuance". In a good game, the decision whether or not to commit genocide should carry a lot emotional gravity and make the player reconsider what they're doing, as well as massive permanent longterm diplomatic penalties (the Armenians still haven't forgiven the Turks, nor will they ever, I think). It certainly should
not be restricted to simply pushing a big red button and reaping some juicy benefits. That defeats the purpose of adding these mechanics in the first place.
Naturally, the game should also offer alternatives which have weaker short-term but better long-term benefits. (e.g.: the Egyptians did not use slaves when building their Pyramids, but paid workers). Civ 6 has government policy cards; this would be a great way to implement these mechanics. I personally believe the Goverment Policy System is a bit too shallow, but if it were expanded into more categories (Religious, Cultural, Educational, Industrial, Economic, Militaristic, Touristic, Diplomatic, Social, Ethical,... +1 Wild Card), then it keeps the players' options open. If Civ 6 really is about conscious decision-making, it is something Firaxis should consider.
Personally, I'm already happy with if Slavery and Human Sacrifices can be added, preferably under the same "kill population for production burst" mechanic we've seen in Civ4. Social Engineering can be restricted to Civ abilities (the Devshirme System for the Ottomans, for instance, and Assyria of course.). Ethnic cleansings are already part of the game, though in a very basic form (where do the people in razed cities go, you think?) and I'm fine with it remaining that way.