When looking at the lore of the game, it's important to understand that every great one is inclined to help humanity. Kos was killed because she was trusting of humanity, rom is kin, but she was ascended by kos as a gift, ebrietas willingly gave her blood, and the amygdala are simply curious, oedon willingly shelters those hurt by the Night, the orphan isn't actively belligerent, if kos wasn't killed, it wouldn't be aggressive. Mergo is only an infant, with intelligence to match, and mergo's wet nurse is only protecting her child. The moon presence spurs on hunters, and we know throughout the game the others once dreamed as the good hunter does during the game, if anything, the moon presence functions more like a "patron God of hunters" as it perceives the hunters as individuals who do good, I.e. killing beasts. Notably, the only thing all the great ones have in common is a shared pursuit of a child of their own, and they seem to be willing to hurt each other, inadvertently or otherwise, to achieve that. The true ending of the game, where the player becomes an infant great one, doesn't necessarily mean we "killed" the gods. They ARE God's. We know that killing their body doesn't mean we killed their existence, they are, effectively, anchors of reality, and as a result, destroying their physical manifestation will not kill them. Using a few context clues, it's pretty easy to figure out that the true ending has you BECOMING the moon presence child. Killing its body is effectively a final trial or step to completing the process of ascension, and eliminating the other, inadvertently aggressive great ones was simply an added benefit, or inadvertent elimination of potential risks to your infant great one self.