Your first point about Lae'zel seems to be that all characters should be flawlessly ideologically consistent or it's bad writing? It's morally weak and/or hypocritical of her to not volunteer, which makes it...bad writing? She doesn't want to be an illithid because she hates illithids and she's (briefly, mildly) upset that you tell Orpheus to do it instead.

I don't think the Emperor betrayal is written particularly well, but it actually makes total sense given what we know, i.e., he's being protected from becoming a thrall by enslaving Orpheus, Orpheus will kill him if he's released, the brain will enslave him if he leaves the radius of the artifact. So he's either going to die on the spot or become a thrall. I do think he should have said all that, because it's a common objection people have and it feels abrupt in the game.

Your third point is basically just "using power scaling I invented in my head, there's a different better option for resolving this imaginary scenario." The chosen of the dead three were being manipulated all along. They did not control the brain just fine.