I don't think Alaya is trying to understand what it is, since that imply thought. I'm not saying that to be mean, I'm saying it isn't capable of thoughts or intelligence, it's closer to a phenomenon that act upon the collective of the unconsciousness of humanity and abides by it. Even if the action itself will bring harm to it, if humanity wants it, it act upon it.
In Kara no Kyoukai, Touko used an example of the "ideal ruler." Pretty much, a great leader unify the world and make it all peaceful and shit. Achieve the perfect balance between peace and competition, no suffering, people lives in prosperously, making advancement, and retaining all that make them humans(unlike QSH), and all that good shit. Nothing wrong with the reign and is great for human future yeah?
The counterforce would have it eradicated. Sure the all of humanity appreciate them and whatnot, but they would have unified envy of them and thoughts like "if only they wasn't there." So then Alaya would then act upon the unconscious wish and snap the fucker's neck.