I think there's a justification of certain kinds of otherwise 'reprehensible behaviour' with context and artistic license. The 'killing' in an FPS is generally fantastical, with you facing hordes of indistinct opponents generally in a very stylised and explicitly fictional setting. And even then, the killing is generally incidental to the plot and meaning of the game itself. GTA, for example, is something of a counter-cultural phenomenon that legitimises itself on the basis of society's declaration of it as anathema. Yet even within this, the 'crimes' within it generally exist as part of a coherent narrative and are once again so far extricated from reality that it's incredibly difficult to make that cross-over from fantasy to reality unless you're mentally vulnerable anyway, in which case any media can promote violent behaviour. GTA in particular is aware of the controversy surrounding it in addition to this as are many of the gamers that come to it - often playing and buying it is tied up with something ever-so-slightly subversive. At least, in my world-view where everything is politically tinted in some way, shape or form.
But there's a line. There's always a line. We wouldn't allow a holocaust simulation game, I think. Or a game where you abduct and murder children. The difference is two-fold. Firstly, there's that arbitrary line where something becomes 'unacceptable' in ethical standards, as already pointed out. In this case, a rape simulator is on the far side of that line and rightly so. I think much of the issue is that sexual violence (Note, specifically *sexual* violence. More young men, statistically, are assaulted in terms of general violent crime, or so I remember. If anyone wants stats / feels like taking issue, please do.) is predominantly against women and most gamers are men, who likely don't see the problem with how rape is perceived in culture. But this is a side-note and not the crux of the issue.
The main point is when the game is *about* a controversial issue or whether it *contains / refers* to it. Many games contain controversial themes - murder, mental illness, rape, genocide and so on - which gain meaning according to those things that they're held in reference to. The one aspect of a picture is defined by those other aspects around it. Rape could be portrayed as negative and traumatic, but its inclusion in a game would be acceptable here. However, when rape is the sole content of a game and the sole stimulus for its creation, then I perceive a problem (Ditto with titles like Manhunt). They have little or no 'depth' to them that would otherwise mitigate their subject-matter. They're disturbing merely for the sake of disturbance or pandering to some twisted fantasy. And whilst I do think everyone should have a right to fantasize about what they want, publishing via mass-media and accounting for 10-20% of an industry is absolutely terrifying and an issue that needs addressing.
The problem with this, of course, is that it hinges upon subject value judgements and non-quantitative data. But still, there are nuances that go beyond 'omg rape' and 'omg freedom of expression' that need to be taken into account in a discussion of the issues. Which maybe one day I'll actually think about in some reasonable depth.