Light and darkness have nothing to do with good and evil things. They're just two different sources or tools, and as such we might be causing bad stuff while bearing said light (especially if we keep doing as we're being told, regardless of individuals like uncle Middy telling us to think for ourselves). That being said, Eorzea having too much light stems from us winning constantly against the darkness representatives. Remember why the light flood happened in the WoDs world: they got rid of all the ascians there and "won". So, yeah, we're about to go to war. But what will happen if we succeed and kill Fake-Zenos/Elidibus?