Honestly, the storyline already has gaping holes in it to accommodate the fact that it's a game, not just a story on its own. For instance, EVERY time the story has you go through a Duty that requires other players, it brushes your fellow players off as "other adventurers" but YOU'RE the hero. Naturally, every player character is a Scion of the Seventh Dawn and all that, every player character is Minfilia's first choice to send out to blah blah blah. There's been a level of suspension of disbelief required from the start. We're trained by, taught by, and surrounded by NPC characters that, if actually outright killed in the story, die permanently. The story never acknowledges our (the adventurers) inability to outright die in this world. If you try to take that into account with the story, of course the story is going to fall apart, but the two simply don't mix.

I'd also like to point out that no one's character is a citizen of Eorzea at all. Even if you started your character in 1.0, your character creation starts you off as on your way in to the city that you chose, and at least once it is mentioned that both the old Warriors of Light AND the new (pre/post ARR) are defending a land that is not their own. The story never acknowledges you as a citizen of any of the three city-states, because you're an adventurer from elsewhere.

Alphinaud more or less recognizes his own huge failings after the whole kerfluffle. It's easy to point and go "ermagerd don't go in that next room!" when you're in the audience watching a rated R horror flick, which means something bad is inevitably going to happen, where-as in a real-world situation you don't hear evil suspicious music queue to tip you off that something's going down. In-world, each of these main characters have a LOT going on on their minds at all times, they don't benefit from the 4th-wall position of clarity every player of the game enjoys.