Cilia, what you're getting at is a little too deep a conversation to be had over an MMO, especially a theme-park one, where our actions don't have consequences or implications. They only show character progress and player-retention.
You mentioned Spec-Ops (haven't played it, but I'm assuming you and I both know it from EC), which is an introspective narrative that talks to the player and asks them questions they don't want to answer. The same cannot be said for FFXIV, which asks us to just be the silent, chaotic good protagonist with a penchant for doing everything and anything in the name of good. Our narrative is being helpful. The quests have NPCs asking us to help them with chores. Heck, even the shady class of the game is just chalk full of good-guys.
Now, that doesn't mean that the question cannot be asked, but due to the focus of the game not being that question, the answer isn't really going to be found and must therefore be inferred or have the gaps filled in by the player. It was mentioned that the logical inconsistencies of the relic questline only obfuscates the morality of the character/player because of the lack of narrative of that morality. That just means it can be taken either way. You are either laying waste to the country-side, harvesting aether from living beings and leaving a wake of bloody destruction behind you or you are going out into the world and purging it of evil, refurbishing/rehabilitating the souls you come across and improving and bettering yourself along the way (in the form of forging a new weapon which helps you then go out and do more good).
Until those gaps are filled in for us, we are left to fill them in for ourselves. The 'hero' aspect, at that point, is really a Fable-series styled hero, where the definition of 'hero' is up to the, well, hero. I think, at that point, the question doesn't become one of morality but one of self-definition.