Killing = / = Murder
Your comparing apples to oranges Killing doesn't = murder. Killing can range from anywhere from Execution, Justified killing i.e. a Hitler, Mercy killing, War, Self Defense, with the worse case scenario being Man Slaughter.
Murder on the other hand usually involves killing a helpless victim, where the victim in question is usually not fighting back or simply trying to get away from you. Being brutally murdered is usually worse than being raped, you want to know how I know; ask any woman if she would rather be raped or brutally murdered. 9/10 I think they'll pick the rape and rape surly is the lesser of the 2 evils once you throw in mass homicide.
For instance I can go on a kill crazy rampage killing innocent pedestrians in the street in GTA and end with punching a hooker to death, are you telling me that's worse then any 1 rape? I don't even have to be playing a M rated game to do this many Teen rated games like Infamous let me kill innocent pedestrians.
You're right we are all going to die, but we are not all going to be murdered, there are people who survived attempted murders and horrific tragedies like mass shootings as well who probably get reminded of there life altering event from violent video games, but ignoring the topic or or removing innocent killings in video games isn't going to make it go away. No one is going to play a game full of rape when they themselves have just been raped, just like no one is going to play a game where the objective to to shoot innocent people when they themselves were just victims of a similar assault.
I also disagree with you on the fact that we are all comfortable with the concept of Murder, there are many more people being shot around the world then being raped and the victim being shot and killed aren't always seen as faultless. How meant times have you heard the phrase "He was a drug addict it was only a matter of time" or " He shouldn't have been there"
Brutally killing an innocent person in cold blood isn't any less sleazy or has any less the need to victimize than rape in fact just the opposite. Not every serial killer is a rapist, yes rape usually makes things worse but it's usually just the frosting on the murder cake. Take for example the Ice Truck killer in Dexter, he never raped his victims he just tied them up and cut their body parts off while they were still alive, you think that's honestly worse than being raped and left alive in one piece?