In Bioshock I and II, I would always pick the "moral" option. I prefer keeping a moral compass in any given situation, real or virtual.
For instance, I wouldn't erase humanity simply because I could, I would do it because I could save the earth by doing so and re-introduce a genetically superior race of humans, solving all of the problems in the old world before it. Most of what I do in any given situation has some purpose or something to gain from it, but that is how I choose to play. Not everyone plays a particular game the same way or for the same reasons, everyone has their own reasons that we, ultimately, cannot see.
As far as I can see, people are getting offended at the "You know, I should be able to kill children in videogames and not get punished in real life" statement because Tony said it and the blunt way that he said it and because they have a gripe with him because of his previous conduct, thus spiralling into an abyss of confused screaming. Of course, Tony shouldn't have made the deliberately provocative drama in the first place, but whether or not we turn into tribal social justice warriors with nothing better to do is our choice.