And that fight is, ultimately, unresolvable. Yuri can forgive herself for not doing the impossible, but she can't forgive God for making the world cruel. And she doesn't have to. The metaphysics here are such that it's her own heavy heart that keeps her here.
Is that okay?
It's probably better than having an actual showdown with God. _The Devil Lady_ could pull that off, but it's super risky. It's very easy to have a broken moral or metaphysical story, and I think _Angel Beats_ is better for choosing not to go there.