I'm not really worried about the quality. It's just that video games are usually very morally straightforward. You are the good guy and oyu must kill the bad guys. There are few exceptions I can think of. Watchmen is more morally ambiguous. It doesn't seem to be something that ought to be a video game.
In the current era of video games?
I know that many games feature something or some group of things that the player has to destroy, but the concept of multiple endings is quite popular these days and usually brings in an element of moral ambiguity, especially when each possible ending depends on who you choose to "save", and how many characters you help during the game. It's not always as straightforward as it used to be.
Just think of Bioshock. One of the main activities in the game involves the choice of whether to "save" the Little Sisters or let them die, and it affects the end of the game.
I've also seen games where the objective is to destroy someone or something, but then the morality of that action is called into question during the storyline.
So yeah, it might not be prominent in all games, but moral ambiguity is certainly seen in some contemporary video games.
It probably won't even be relevant to this game, though, since it's in a different context from the actual story. But who knows, maybe they'll release another part where you're Ozymandias, and your actions determine whether you get the "I did it 35 minutes ago" ending or the "Oh crap, I should have done it 35 minutes ago!" ending.