I like a lot of the ideas presented here, but I think the trap to avoid is making everything anachronistic. If slavery is culturally acceptable om the in-game world, it should be treated as such and not be all "hint hint, nudge nudge this is wrong". If the abolitionists are committing acts of terrorism, treat them as such and not as misguided heroes. Is the slave trader a legitimate businessman? Treat him as such as well and not some secret monster. Same goes for any of the other '-isims', allow the ideas to be present but don't try to railroad the player into a specific line of thought. Show, don't tell, and leave the player to figure it all out on their own.
::Edit::
Also something that could be played around with: Seeing how souls are persistent and eternal, or at least outlasting the bodies they currently inhabit(?), I'd like to see something along the lines of persistent karma and individuals having to reap the consequences of previous lives be they good or bad and irrespective of how good or bad they may be in their current life.