But I don't think that rape is being used here as a shorthand for a complete monster, but rather as a part of his actions as that monster, if that makes sense. In the story Joker doesn't resort to rape just for the sake of rape, but it is a part of the awful mind game he plays, ripping apart the man who idolizes him. And given the context of the situation, it goes pretty close to the situation you described.
To degree that rape in itself is automatically sexist as a story vehicle, even if it has been overused to a degree at a certain point of time, is kind of limiting, because there a monsters and villains in the real world who do that. By the same degree I could argue how I never want to see theft in comics, because we've seen so many thieves in them. And yeah, there is a difference and it is all about context, but if I understood you crrectly, you are automatically judgind it's use here without taking that context in to account.