I know what I'm asking is far and above the sort of thing an MMO deals with. MMOs are simple, "Kill the bad guys, get your phat lewtz." No consequences to live with, beyond what happens in the MSQ. Even so, I thought it'd be fun to try and ask people the same uncomfortable questions Spec Ops asks players.
(And what the kupo is EC? I played that game meself! Hence, why I do not really feel like a hero... and am seriously gonna Dark Knight it up in 4 days.)
There is no moral complexity to the game. The bad guys and good guys are cut and dry, clear as night and day. The PC is the good guy, "Eorzea's hope" as Minfilia so succinctly puts it. Anything you do is justified or excused by the narrative because it's for the "greater good"... even if that's mindlessly slaughtering sentient beings for a glowing stick because a musty book told you to do it.
Is that justified because those same sentient beings are the thralls malicious, planet-killing gods and goddesses? Maybe. I'd wager most players just do it for fun and profit, though.