Didn't we get two canonical confirmations that Beast bringing the teenage versions of the original X-team into the present broke the multiverse? (quoth Beast: Ta-da) First, the Watcher himself told him so by getting into his bedroom (nope, not creepy at all) and giving him visions of all the universes, both good and bad, that he had killed. And later, in one of those bi-monthly situations when one or more people get cosmically omnipotent or thereabouts, he made the calculations himself and confirmed it.

So I'm calling shenanigans on the the Beyonders weaponized the Molecule Man crap. Beast did it (in his defense, he was dying at the moment, and it was an hilarious thing to do).

Things get interesting after that. Beast being an X-Men, he won't give up just because he screwed up at a cosmic level. I mean, that's what they do: they screw things up at a cosmic level and then they sort of fix it, mostly. Therefore, he's Rabum Alal (oh, and in the Black Swans' language, that's more accurately translated as the Predator, the one who culls the weak). Because he didn't find another way to save universes, he keeps destroying Earths to buy time, going to other universes to find increasingly powerful weapons. He's no Doom or Reed Richards, but there's an awful lot you can do if you're a genius that has seen them work and has given up on small measures. Needless to say, the accumulated guilt has driven him quite crazy, but there you go.

Bottom line: Beast is a doctor. He knows that sometimes you have to cut something out to extend the life of the rest. And there's so much blood on his hands that the marginal guilt of each new genocide is negligible.