What is a genocide when all you erase is memories and not the soul themselves, who just reincarnate later? What is a mortal life to a being who will see that selfsame soul come back to an eternal state later on?
Emet-Selch himself says it: "I don't consider you to be alive, ergo i'm not commiting murder". He's just mending the broken souls and healing the world, in his view.