I think it's somewhat problematic to prejudge an individual based on a general and cursory observation of a species.
If you transform, the Narrator specifically says the Emperor is unique and you could be too.
(I personally know many humans who also discard friends who are no longer useful, by the way, so this behaviour is by no means particular to mindflayers).
Of course, in the real world this would be a massive problem. But I'm just talking story-wise. And in the story we get many cues that a mind flayer is something you don't want to be. The reason being that the parasite will take over and you won't be yourself anymore.
Yes, the narrator tells us the Emperor is unique. And he is.... until he isn't. As soon as you choose to free Orpheus he'll immediately switch sides and becomes everything he was fighting against. Through out the story he tells you that freedom is the most important thing to him. But when you play a character who thinks that freedom should also extend to Orpheus, he will join the brain because you didn't do things his way and thinks you're going to loose. And that leaves me to think that controlling you was a bigger motivator than the freedom he says he wants.
