One thing that is worth considering -- and I'm pretty late in jumping into this so my apologies if this has already been covered -- is that once upon a time, violence was a big deal in games. We're going back a long ways, but when Mortal Kombat was unleashed on the world back in 1993, it did stir up a lot of controversy. It's just that -- like a lot of things in life for better or for worse -- this stuff often becomes the de facto standard as many people that aren't overly concerned about these activities move on.
But for what it's worth, many people today are still concerned about violence in video games. Mind you, it only becomes a hot button issue when a mass murdering gunman is suspected to like video games, but it's not like everybody on the planet has embraced violence in video games. And even people that often aren't up in arms about the prevalence of violence in video games will often concede that violent aggression is probably an overused mechanic in gaming. Recently -- and though I haven't played the game myself -- I noticed a lot of people criticizing that the shooting in Bioshock Infinite was at odds with its narrative. Given that, it's important to me that people realize that the over reliance on violence does not go unnoticed.
Also -- and I'm quite certain that I'm not breaking any new ground here -- I think the difference to be noted is that I think people would be hard pressed to explain why being able to rape would be mechanically necessary from a gameplay perspective. Killing really isn't either, but unfortunately so many games are just centered around the idea that the focal point of the title is a violent conflict where killing is inevitable. That still leaves narrative, mind you. So I can't completely toss out any arguments that a character raping another isn't somehow integral to that game's story, but I'll just kind of recuse myself from that discussion as I'm not the biggest proponent of narrative as an important part of gaming to begin with.
And finally, getting back the original observation about the length of time separating Mortal Kombat making waves on the scene way back, it's worth noting that this too may become accepted and uncontroversial for people out there that think it's important for creators to be able tell the stories they want without fear of the angry populace lashing out and threatening creators that aren't ready to stand behind their work. Personally speaking, I could do without characters raping other characters in my video games, but if creators stick to their guns and this becomes more common place, I wouldn't be surprised to see that rape in Hotline Miami 10 in ten years is almost completely uncontroversial.