'We' are in an entirely different dimension. 'We' created a representation of ourselves that was not as Godlike as we naturally are to those people, in order to interact on a more equal basis. There is no hint that Primeworlders actually control events in alternate realities, merely that they are privy to them, unconsciously.
From a primeworld point of view, Superboy Prime has killed no one. No more than I have killed if I write, "Rocks fell on the planet Earth. Everyone died."
If the opposite were true, how many more mass murderers would there be on Earth Prime? Shouldn't they go after Geoff Johns Prime? Didio Prime?