There is a Game called "Train" by designer Brenda Brathwaite. It starts out with an easy enough task, move trains along rails to various stops, collect pawns, try to get the most fastest, and then deliver them to the destination. Seems like a fairly usual type of game. Until the end.
Spoiler Warning: A card is removed, and it turns out the name of the destination is Dachau. The players have unwittingly been competing to execute the most people.
"Looking up Holocaust Train Game" or the author herself can find a large number of articles about peoples reactions to the game and the aftermath. Here's One, and an interview with the designer, and a summary of a Game Developer's Conference discussion of it.
The game is often presented as an "art installation" in a museum - a fresh piece of glass is broken as the game is set up, and then people are invited to play, unaware of the twist ending. It does an excellent job of demonstrating what is known as "the banality of evil" - up until the end, you're just another bureaucrat/conductor trying to maximize cargo. After the question is, if you play again - how - or do you? Couldn't you have opted out at any other time? As the classic movie quote goes "The only winning move is not to play".
Of course, like the "Third Wave Experiment" or the famous "Stanford Prison" and "Milgram" studies. There might be some potential for people getting too far into it. A reason why Russian Front WWII games or Warhammer 40K (where everyone is a genocidal evil, especially the good guys) is because no one is rooting for one side or the other so politics can take a back seat to play. Release forms might be needed, or perhaps splitting the lesson over a few days to lessen the total impact. Of course, there will always be people who take it the wrong way, or revel in being a warlord in a game.
Junior Generals isn't RPGs, but it is wargames designed to teach children about the choices made during famous battles - ranging from Kadash (1300 BC) to Ia Drang (1965). I'd love to make one for that site dealing with PT boats, but every time I think about it, it gets too involved for easy play. (Since the boats were often used for night-time sneak attacks, you need spotting/silent running rules, in addition to torpedo firing and turn arcs.)
I certainly agree that this would be an interesting way to teach a class. Heck, when someone who doesn't know about RPGs asks what I design, I tell them education tabletop simulations rather than trying to go in depth about role playing - and that is what I'd like as paid employment.
Games of imagination are never truly done. Yet tomorrow we shall start another one.
The controversy over D&D suicides gave the whole insustry a bad rap. Although a game about social issues would certainly be interesting, it will probably just give role players an even worse reputation.