Yes, rape is a super evil thing, but if a bad guy and wanted to torment a good guy that he couldn't touch, it's certainly something that would be in his playbook. Yes it's been used ad nausium, but so has murder, torture, etc. Yet we don't complain about those...unless they are against women. I'm not going all men's rights on you, but if rape and torture of women is such a bad thing, you damned bet a bad guy will use it.
One of the problems is that rape is depicted almost exclusively as this ultimate evil. It's done by villains as this proof of their evil, or by characters whose only identity is rapist. In reality, rape isn't always as stark as that, and therein lies the problem. We see all sorts of levels and motives for murder. Characters who are killing for fun, who are killing with an evil purpose, who are killing with an ambiguous goal, etc. Same for torture, plus we see all the forms of psychological torture that aren't done by evil masterminds, we see abusive parents, asshole teachers, corrupt authorities, etc. Torture and mistreatment covers the range from Saw down to Roald Dahl adults. And society at large generally recognizes and confronts all these different forms of killing and abuse. We've got blind spots, and problem areas, but not nearly as much as rape.
Rape isn't treated the same way in depiction in most fiction, and more importantly isn't treated the same way by our culture. As a culture we teach "rape is bad, don't rape", but we also promote the idea that rape is some unknown guy jumping out of the bushes at some woman walking alone at night. Our culture is pretty damn terrible at recognizing all the other forms of non-consensual sexual activity that should immediately be recognized as rape. Hell, just the fact that, until recently, rape was legally something that only a male could do to a female victim makes it a very polarized crime.* We, as a culture, are just barely beginning to start discussing what consent is, what it means, and how to deal with rape when it's not an extreme and easily defined case. Until we reach a point where our cultural discussion of rape, and it's depiction in media, starts to reflect more fully the issue as a whole, it's a huge problem to continue to depict rape in it's most extreme, simply to show off how evil a character is. That only serves to reinforce the notion that rape is only the extremes.
*And that's a second big problem. The fact that rape is, by and large in our cultural understanding, a crime that is committed by men against women, gives it huge connotations well beyond just the evil of the act itself. Murder is done by anyone, to anyone. Rape is done by a man, to a woman; at least as far as the average person is concerned. It's a crime that targets a minority, and in the case of The Killing Joke, is being used to violate that minority figure, in order to provide motivation for heroes who are literally in positions of power. Would you be okay with it if Perry White's adopted black son were sold into slavery in order to provide motivation for Perry and Superman? Or would you be bothered by the cultural implications of making a black character a slave in order to outrage white people?