Emet-Selch at least admits the moral relativism involved, and Alphinaud might be flower and idealistic about it but his core point is that Emet's elitism in deigning to draw the boundaries of what life matters is bad enough, but the one's he's fighting for are already gone.

Over 75% of Amaurot's surviving population was consumed by Zodiark and all he cares about is freeing those souls. If the Great Sundering had never happened, if Hydaelyn had never been summoned, the council would still be trying to sacrifice the life that came after to restore the "better" life that came before.

Emet-Selch's own people didn't unilaterally buy into this logic, this worldview, or this plan. Emet-Selch's own people created Hydaelyn to stop it. Divided and diluted though that life may be, it is happy in being so and it is alive right now; it has every right to take a stand and - if they can manage - bring everything Emet's side stands for tumbling down.

War only works if both sides think they're right.