That's true enough. In fact, one of the reasons that chivalry was created was to put restraints on what a person could and couldn't do in terms of violence. One theory is that part of why the chivalric code came into being was to protect noblewomen from male violence.
Specifically in terms of the game, I don't think it's appropriate because having an option to rape is just an arbitary choice, and many modern players (women, in particular) will feel uneasy about it. Equally, saying character's soldiers have the option to rape because it happened in history will only carry the argument so far. For example, there's the 'Kill, rape, and burn' option. But there isn't an option that says 'Kill babies' or 'kill everyone with a different skin tone'. Both of those things happened in medieval times (and are still happening) but there are no options to do that in the game, presumably for moral reasons.
Odds are the TLs aren't doing the raping, but the troops are. And the chivalric code was far from universally adopted... raping certainly existed back then, as it does today. Warfare always generates a lot of it.
Maybe there should be a "kill babies" options. As for skin tone, I don't think that medieval europe had quite a lot of that. Different skin tones were in foreign lands. At which point any case of killing was killing different skin tones.
