He didn't ran away, he just did his job as a tuner. The world was going to shit since both MU and the normal world was separated, it was going to be destroyed soon without a tuning.
What he did was just putting the world back to his original state.
Anyways I don't even know why some people talk about this, in Eva the ending of EOE was necessary because of everything that happened before, it was coherent with the whole thematic behind it
Rahxephon is different, the "goal" of the anime, the story it wanted to tell was different.