I think you can easily accuse most games of lazy, tepid writing when they use threats of rape or murder as shorthand to imply that a character is evil. But that's very different from it being a misogynist trope. The problem with Sarkeesian's arguments is that they focus exclusively on the trope as it relates to women, intentionally stripping it of context to make it seem more targeted than it is.
For example, I think it's uncontentious to say that in video games villains are characterised as such through a WIDE variety of lazy tropes:
-has a posh accent, especially British? WATCH OUT HE'S EVIL
-is slightly intolerant towards elves, qunari, etc.? WATCH OUT TOTALLY EVIL
-extremely or ostentatiously wealthy, contemptuous in any way towards the poor? OH WAIT I KNOW THIS ONE HE'S EVIL
-casually threatens to kill someone's family? OMG LOOK OUT FOR THE EVIL
-kicks a dog or treats any animal unkindly? MAN, SO EVIL.
-threatens sexual violence towards women? OK GOT IT, WAY EVIL.
All of these examples are used extremely frequently in games. It's absolutely not the case that sexual violence towards women is the "go-to" lazy writing trope to make game villains seem evil. Of course it's going to look that way if you build a supercut of JUST THOSE examples, though.
The only possible problem with this (besides the problem of lazy game writing) is that threats of sexual violence towards men are not a frequently used trope in games to characterise villains as evil.
There's a few reasons for this, though. Firstly sexual violence against men just isn't as big of a problem in society as sexual violence against women. Accordingly, it doesn't resonate nearly as much with audiences.
Secondly, and more importantly, since most villains are male (a problem in and of itself, but a separate one), threats of sexual violence towards men would often come across as homosexual, and I think game writers want to steer clear of portraying homosexuals as rapacious or sexually predatory, for fear of offending that demographic.
In the case of a female villain, threats of sexual violence wouldn't really make as much sense, although I wouldn't object to them being included more often. It would have been interesting if Knight-Commander Meredith threatened male Wardens with castration or rape by her templars. Totally out of character, though.
In general though, I think the main problem is lazy villain writing, not misogyny.