Qliphot and the thing that pulled Michael are two different thing yes, it's was clearly said in game already.
As for the queen of the sky being that entity now it's indeed very likely based on what Aos said , and he couldnt be talking about his people since him and Danu turned them into Sidhe, so it dont left a lot of possibility .
Aos also did say something else very interesting, he didnt want to talk about it because it would be blasphemy to the highest order, so personnaly i'm not fully convinced it was done by apostles, they hare the highest order, so i wonder if it isnt something that would have been done by the crones to the queen (or her body after her death ) at some point through some ritual like the alt humans turned into those tendril to protect them from the Qliphot.
another thing that made me think that is that even though these tendril were made at a point were they already lost (Apostles started terraforming), they wanted to protect themsleves from the tree, not the sky, even though it seem to protect them from it too, and it's noted that they emit an eerie glow similar to the sky.
As for Michael killing it/her at this point it's ridiculous though,because even if we assume she is weakened in this state, A rank monster (who are far more powerfull than Michael would be as a level 3) still fear it, so he wouldnt stand a chance and i'm realy curious how he did survive up there.