well, for starters, it's not, at least I don't think it is. Killing a person is a more reprehensible act then raping them. But some will argue against that stance, and whatever, i don't want to argue. They're both horrible. Rape leaves a living victim who will have to live with the act for the rest of their lives, murder just leaves a hole. Murder more hurts the people who are close to your victim, less the victim - you're just robbing the victim of potential, rather then potentially ruining their lives. Although still, having said that, my personal belief is that Killing is worse. It's the ultimate bad thing you can do to a person, just turning off their future and emotionally destroying all the people they love. That's worse then Rape, which is more a personal destruction thing - close friends and family will hurt, but nowhere near as bad as the victim, and not as long. Murder just has a larger effect.
You mean in games though? forgive me, this is the off-topic forum. In pop culture in general, it's because we idolize soldiers. Our greatest stories as human beings are our stories of war and conquest, and war and conquest involves a lot of killing. It would be silly to, on one hand say "support our troops" and in the other say "death is universally wrong". You can believe either, but earnestly believing both is a little incongruous. We have a generally conservative government that's roots are in religious dogma. It's no Iran, but it still has echoes - religious conservatives of almost all religions tend to see extramarital sex as wrong, and rape to be reprehensible (to differing degrees and with different opinions of the victim). But all religious texts and lessons, even the ones they teach children, are steeped with death.
Games have a special case though, because no matter what they are today, they were sold to americans in the 80s as toys. Before then, there were more games of a pornographic nature - Adult Game Designers were making Adult Atari Games for Adults. Nintendo had control over their software, so that never happened on the NES. America (and western culture in general) still see games as glorified toys. In the beginning, actual "death" didn't happen very much, and when it did, it tended to draw you out of the experience rather then pull you in. Mega Man shooting Bad guys, slowly, over time, became Duke Nukem jumpnig around in his pink shirt, then BJ Blaskowitz blowing away away Nazis in Wolfenstein 3d.
But for CERTAIN, there's no reason to mix real life death/rape with game death/rape.
That's what the idiots like Jack Thompson do.