Why does Ayato kill Elvy, Souichi, Mamoru, and the others?
As sad as it is, when Ayato merged with the RahXephon, he simply lost control. When he merged with the RahXehon, he became a sort of god. He’s no longer human, and cannot go back if he wanted to. As a side-effect, Ayato lost control over his power and ended up killing everybody without even thinking. In other words, he wasn’t conscious when he did this.