Hmm. No, I don't agree.
Murder is largely seen as a problem. Rape is not. In the US, for example, we see political candidates that entertain the idea of the death penality used for women that have an abortion, and at the same time think laws against sexual assault are too harsh, and major politicans openly mock rape victims in public. Even now, a woman that speaks up about being assaulted faces harsher consequences than the assaulter. Take several of the public figures who even admitted to doing it: Several are making comebacks after less than a year, with people cheering for that, while the victims get blacklisted. Goes for male victims too, by the way (as men can get raped too - you just don't see it glorified as often as the rape of women is).
I'm sorry, but as a culture, the difference between murder and rape couldn't be bigger.
...and the idea that murder in games is fine is something I wouldn't even agree with. I'd in fact argue that a lot of games contribute to attitudes that murder of some people isn't a problem (especially of non-white people!), much like the TV series "24" contributed to torture being more acceptable in the US (down to politicans using 24 as an argument to defend torture). Media doesn't exist in a vacuum, it's a reflection of culture.
And lets be frank: I don't think it's mean to think badly of people that want sexualized rape depictions in media. There's one thing to have it as a plot element, and another to use it to titilate.
I think there's also a difference in that some depictions of rape, in addition to being meant to be erotic or visually appealing for the audience, also eventually show the victim (on some level) enjoying it, which then links to real life accusations that a woman that isn't covered in blood and bruises wasn't raped because she didn't fight back hard enough. It's incredibly rare to show a murder victim enjoying being murdered, even if the illustration of such violence is shot in an appealing a way as possible- the erotica is for the viewer and perhaps the killer, not the victim. That's what makes people question the viewpoint of the creatives behind it- the erotica of violence doesn't come with the occassional sense that the creator thinks it's erotic for the victim too.
Fantasies of revenge or power are one thing, but showing the victim being overpowered and then starting to like it is what then adds an additional creepy justification (that is often joked about by abusers) to rape on top of the power fantasy that is also present in violence. I'm not saying that's present in the manga under discussion here (I haven't read it) but it's the difference between some segments of rape vs murder in terms of message to the (often presumed male) viewer and implied view of what the creator is thinking, or at least why people look at it differently.
You've also got the societal sense (at least in terms of fiction) that being a sanctioned killer (for whatever perceived-morally-correct reason) means killing is perfectly fine. If a knight/gunman/ronin/adventurer etc is killing bandits/mutants/monsters because they keep killing peasants in a world with zero enshrined courts of justice, for the most part, people are on board with that kind of frontier justice and can get behind the art of their skill at despatching the 'baddies'. There's no scenario where admiration at the skill or erotica of rape works on the same level of (however misplaced or assumed sanctioned) justification.
I mean, I think violence in games is something I think we do need to look at as the immersion and visual fidelity continues to evolve, but I don't see the comparison to rape in this case.
When we talk about violence in media, we are usually talking about characters on screen/page for a few seconds and dead moments later as cannon fodder, and there's a discussion to be had about the consideration of people as such, but it's very different to protracted periods of abuse. Perhaps a closer comparison would be someone trying to make domestic abuse as appealing and visually exciting as a thousand stories, films and games about being a soldier killing greater numbers of less skilled enemy soldiers, something that just sounds so very, very wrong, but for some reason the fascination with rape-as-erotic-entertainment continues.
On a related note, I thought Quiet's torture scene in MGV was rubbish, in that the scene can be summed up as the creator's idea of 'what a great pair of tits being zapped'. Her face covered because, of course, neither the director or the viewer wants to look at the only signifier that the woman isn't enjoying being naked, tied up and tortured while being ogled by the camera. If the plot required it to be a bloke getting zapped, somehow I get the feeling it wouldn't be shot as 'how weirdly sexy is this!'.