Do you scrub your world of slavery and other historical crimes?
Generally no, with the exception of forced sexual assault.
If so, how do you encourage heroism?
I don't. The players can play what they want to play; and if they play heroes that's fine, and if they play not-heroes that's fine too.
If not, what do you do to mitigate the real potential discomfort such subjects can cause? Do you make different decisions based on the specific game or setting?
These days I only run one game and setting, and it is what it is. My hope and expectation, somewhat harsh though it may be, is that people will leave their hangups, egos, bad days at the office, etc. at the door when they arrive at the session, and spend the time relaxing and enjoying the game absent all those real-life downers, while recognizing that in the end, it's all in fun.
Do you run historical games, and if so do you "soften" history to make it palatable?
I run what I run, based somewhat on faux-history (or pop-culture versions of history - Herc-Xena for the win!) mashups, warts and all. I don't try for historical accuracy, but I don't paint things over either. Hang around long enough and at some point or other in my game you're pretty much certain to encounter slavery, colonialism, genocide, torture, mind control, racism, various other -isms, and any number of other things seen as unpleasant in the real world; and it's up to the players-as-characters to decide whether to fight these things, or join in, or just walk away.