The beings did wipe out humanity, the CYOA states it pointblank. They didn't do it on purpose, so I'm not saying I unilaterally hate the Beings, though the mindless shells as pets gives me some weird feelings. I mean, after all, while I'm pretty sure Chernovy lacks Beings, Hei Lan is headed by a small group of them. If I was hostile to Beings I'd have to be hostile to Hei Lan, and that'd be stupid.
You say that, but people don't suddenly switch the color and nature of their essence and aura, gain a level of essence, a never before seen essence form, ten times the lifespan, and have their familiars turn into Cthulhi either. But what do you know, all that's happened with Chernovy.
Putting sapient beings under control is wrong, again, no evidence really points to them being berserk. And no, I don't think the Cordat and Inu lowlevels know or care, and I doubt the higher ups would lose any sleep, over an incarnated Cherny getting leashed by accident or 'accident', And once that's happened, you've doomed an actual person to working as a slave like the mindless.