Sexual assault would seem to fit in the world of Hotline Miami just fine. It's a brutal world, and I don't see a reason to draw arbitrary lines set from the outside that one kind of violence is ok but another is not. Let the developer determine that. I don't like the idea that all video games (or any medium) need to be cleared of all triggers. That's just stifling to creativity, an amount of freedom is required for the medium to grow. I know it's not pleasant, but if you can't stand it, don't play it? The idea that it can't exist seems needlessly restrictive. Rape is a horrifying part of human existence but that doesn't mean you can't show it, it just means you should deal with it in a manner that doesn't belittle it. I agree with the thinking behind these complaints to some extent but I don't like the solution, to just purge it completely.
But speaking of how you deal with it, it does sound like the scene is just poorly handled. It doesn't clearly communicate what's about to happen, control is taken away from you, and you're *forced* to rape her? That doesn't work for me. At the very least give us some options. Though I seem to remember that was never Hotline's strong suit, I once tried sparing a guy but I couldn't leave the area until I killed him. Maybe that form of storytelling works best for them, but I don't think that's playing to videogaming's strengths.
RPS' headline is pretty misleading by the way. All the dev is saying is they'll re-assess after testing in the full game. That's something that probably would have happened anyway. That interview is really hostile anyway, good on the dev for keeping his head.