Don't mix up comics with these video games. Personally I don't care if Darkseid were to wipe out most of Earth before the Justice League of America stopped him. Somebody will write another story where that never happened. The bigger crimes that supehero comics commit is the stunting of progress in face of the scientific leaps they reveal. People in DC and Marvel comics should already be making the step of migrating to other planets and all that science fiction stuff. Instead they have us focus on the adventures of a few superhumans who decide Earth's fate.
That is very different from what we do as players in these games. We're each given the ability to determine the fate of nations. If Bioware expects us to choose to just kill millions because one race lost its glory then they're teaching us to become immoral. It's simplifying the issue as 'breaking a few eggs to make an omelette'.
You'e missing my point. To simplify, in comics you have 'small-steps-heroes', people who try to preserve the status quo and who obsess over the 'I have a code and I won't kill' things, etc. It's done for a variety of reasons - to be audience-friendly, to be politically correct, whatever. But it need not - and indeed is not - the case in Thedas. It's true what you said about the chosen few deciding the fate of an entire world, but that's not my point here anyway.
Thedas is not an idealistic universe - it's fraught with difficult choices, sacrifices for change, and with the status quo being a bunch of mundane, stuck-up nobles and commoners infighting even when they should unite. Thedas is where the Herald of Andraste gets turned upon by the nations he/she saved, and where his/her heroic legacy could potentially end up to be nothing besides one less arm. The inquisitor, hence, should be played to be morally flexible, having a wider notion of good and bad, right and wrong. Indeed you're not playing Dragon Age right if you're held up by this limited view of morality.