I think it's worth looking at the events leading up to the showdown on the First.
  • Igeyorhm wrecks havoc on the Thirteenth, killing off nearly all of the inhabitants of that world with the resulting Flood of Darkness and turning them into aether-starved voidsent, a state that their souls have been stuck in for the past 10000 years.
  • Elidibus recruits a couple of survivors and attempts to use them to manipulate Ardbert's crew on the First. Ardbert spares Cylva and kills Mitron and Logrif, causing the Flood of Light and turning Mitron into Eden.
  • Elidibus tries to manipulate Ardbert's crew into causing havoc on the Source. After listening to their story, Minifillia voluntarily returns with Ardbert's and friends as the Oracle to help them hold back the Flood of Light.
  • Stymied by Minfilia's efforts over the next 100 or so years, Emet approaches the then leader of Eulmore, and infuses his unborn son Vauthry with a lightwarden's essence, so that Eulmore could speed up the process of aetherically corrupting the people on the First into lightwardens.
  • Elidibus makes a plan to augment Emet's efforts on the First by unleashing a deadly chemical weapon, the Black Rose, to annhilate millions of Eorzeans as well as his own Garlean people.
  • Elidibus is foiled when Zenos shows up as an unnamed Garlean soldier, and literally stares the Ascian down until he flees in panic, leaving both the body and his pride behind. Zenos destroys the chemical weapons.
  • Emet hatches a plan to aetherically corrupt his long lost friend, the player character, into a Lightwarden in order to trigger the Eighth Umbral Calamity. It backfires when Emet is impaled with extreme prejudice by that selfsame light.

I can understand if you want to root for the villains. They're really entertaining characters. But I don't think that you can use moral indignation to justify their actions. You can sympathize with Emet. You can understand why he did what he did. But you can't really say that it was anything other than self-serving and evil. He's a fallen hero, and Endwalker was his redemption arc of sorts.

The only way that you can try to justify what they did is by trying to distract as much attention away from the Ascians' actions as possible. But why bother? Just embrace his villainy. It's what makes him fun.