I was pondering the same question, and the conclusion I reached is that it doesn't matter. Killing, death, and even murder, are an unfortunate but expected, and even necessary part of the game that is D&D. Rape is not. It belongs in D&D as much as it belongs in Monopoly or Candy Land (at least as far as overt application by players and DM).
I disagree. That's not to say I believe rape
belongs in D&D, I could certainly run a D&D game with no killing, an intrigue, diplomacy-based game wherein the players find clues, solve puzzles and generally attempt to resolve any potential "encounter" without violence.
D&D is based out of a psuedo-medieval fantasy, unfortunately for all the high-minded-ness that D&D attempts, it is not without artifacts of that medieval lore. Medieval life and medieval lore was incredibly dark. Life was cruel, brutish and short. People were terrified of their own shadows, even the supposed forced of good in the world often caused more violence than they prevented. Rape existing in D&D is an unfortunate side effect of the fact that D&D draws its creative inspiration from a time when rape was common. When anyone lower than your own station and especially women, or anyone weaker than you was property and a target for your desires.
Rape has a very specific place in D&D, just as everything else does. I have had campaigns wherein NPCs have been raped. This was a tool to motivate the players, to get those otherwise on the fence to go "woah". A sledgehammer to make my point that the bad guy is indeed a bad guy and that is bad and only
you can do something about it. I apologize if I ramble I will attempt to tl'dr:
tl'dr: Rape, like all bad things, has a place in D&D, if only a niche and perhaps extreme place. But to deny that, to claim that rape has
no place in D&D is I think, to deny history. To attempt to whitewash reality in favor of a more pleasurable alternative, but I do believe that it is only by recognizing that this dark side in our own history exists, that we are able to move away from it.
I'm in favor of non-alignment games, where shades of grey reign supreme, and there really is no "orcs are always evil, so it's okay to kill them" attitude. I enjoy being faced with moral ambiguity and then the party having to actually decide how they wish to proceed. Of course, in alignment-based games I like to constantly repeat that orcs are always evil, and that we should not hesitate. I also like to challenge the stunted morality of the goodie-goodies.
I tend to agree until the very last point. I like to present situations that offer the chance to question your own morality. You may choose to question, or you may choose not to. I don't like to put my players in a position where they
must challenge their morality, though it is nice to see change over time through reaction and learning more about themselves and their characters, it is also equally interesting to watch characters double-down on their initial beliefs.. "Change" in a character does not always mean
improvement, but it is none-the-less interesting.