It could be pointed out that the threat of rape against females is overused in storytelling. To show how "villainous" a villain is - he will rape a woman.
It's funny because I find this trope more offensive to men than to women. If you've read a story or played a video game in which a villainous female raped another person (any gender) - you might do a doubletake since it is such an underused trope for female villains.
"Bad guys" - quite literally bad men - tend to have their level of evil-ness measured by how rape-y they are. As if a man who is evil couldn't be opposed to rape. It'd be more interesting to see an evil male character who is legitimately against rape.
Is killing and the threat of killing also overused? A lot of games consist mostly of killing. And in a lot of cases, the evil guy kills innocent people. That is pretty much accepted. Torture is another trope widely used. Overused?
In the end, there are a bunch of tropes which are a quick way of making it very explicit that this person is evil -- and they get used over and over again.
To single out rape and claiming it's sexist sounds extremely biased to me.
Rape threats by females against males are much harder to work with, because of the physical strength difference. I've seen it (Buffy comes to mind: WillowVamp on Angel), but it's rare, because it's also much rarer in reality. As for DA, there is some ambigiouty of how Fenris was mistreated. A different angle is the mind-control magic by lust demons -- it has touches of mind rape. Then there's the dark ritual where Morrigan basicly requests to have sex with a person who hates her, in order to to receive his child. Not rape, but definately uncomfortable for Alistair.
As for the villains being all rapey: I think Bioware has a lot of very nuanced evil characters which aren't all that rapey. Loghain is a pretty good villain, and so is the Arishok.
So I think there are a lot of variations of what BioWare does, and just saying "oh, rape against women, sexist game" sounds to me like "oh, there's killing, horrible unethical game".
But to acknowledge that and look into the story and the context of the game requires an analysis which is far, far far beyond the superficial level of criticism that femfrequency offers.