I'm still convinced that Innocence is a parasitic force from space and The Noah weren't outright evil originally but rather the only survivors of the apocalypse which Noah caused creating Black Matter to destroy The Heart. Black Matter potentially distorted and corrupted Noah and the others as well.
Innocence is the thing that destroyed Noah's world, we were shown The Pillar in Roads's flashback when she talked with Cross during Allen's long flashback. People, please, reread.
Black Matter probably was created to fight it, but more like after the fact, Innocence was scattered and Noahs had to rebuild the world from scratch. They are progenitors of current humanity and that's why any killed Noah can manifest again in random person.