The comic elements added to the rape scene
At first I was really offended by it, but then I realized, that was the point.
Rape happens so often in movies, we're desensitized. Kubrick re-sensitizes the viewer. Kubrick could have gone the route of movies that take themselves a little bit too seriously and had just portrayed a plain rape scene with dreary colors, heft in directing and harrowing music. Kubrick could have just followed the rules but he wasn't trying to be an ordinary customer.
The reaction to most rape scenes is pretty much "aw man, that sucks". The response that TCO elicited was more along the lines of "THIS IS HORRIBLE!!! I CANT BEAR TO WATCH IT!!". That's how rape should be received.