The full frontal male nudity in that game is hardly the most disturbing part. If anyone complained about it and not all of the other awful **** that happens in that game then I would argue they probably have mental issues.
The thing is, though, violent themes have already more or less been accepted in society. Having worked at a movie theater, parents in general were always far more concerned with Little Timmy being exposed to sex and nudity than gratuitous violence. A guy can get disemboweled and decapitated and no one cares. Show Dr. Manhattan's genitalia and suddenly everyone's up in arms, walking out in the middle of the movie all offended.
What's interesting to me is that the developers of Outlast didn't shy away from anything -- they could've easily slapped a few scraps of clothing on their characters and avoided any potential outrage, but they didn't. I was impressed not only with that move, but also the gaming community's generally mature response to it.
I digress, though. It's ultimately up to Bioware, but I agree with FF and others that if you're gonna do sex scenes, even just brief scenes to imply what's happening, there's a way to handle the nudity tastefully -- most notably, with camera angling.
There's really no denying that the way they've gone about censoring things in the past with clothing, etc. only made something intended to be deep and meaningful turn laughably stupid.