Of course, in the real world this would be a massive problem. But I'm just talking story-wise.
Consequences differ in the sense that people here are fictional. But the issues remain.
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...? Don't you think that's incredibly bizarre? His entire life and life as an illithid has been about his desire for freedom. His endless travels and seafaring. His escapes from the Elder Brain. And now he gives up and joins it, after spending the entire game trying to convince you to destroy it?
See, THIS is where I think Larian's writing falls apart. From everything we know about the Emperor from the story, we know that his primary values are freedom and survival. So in a way, him joining the Netherbrain indicates that he thinks his chances of survival are better with it than with us. Yet, his pivot from freedom to survival is barely a 1 second line. When I tried it in my game, I barely even heard what he said, then he was gone. We SHOULD have been given a chance to persuade them to work together.
And that leaves me to think that controlling you was a bigger motivator than the freedom he says he wants.
Controlling you to do what? He's not doing it for fun. It took massive risk and effort for him to communicate with us while he was fighting off both Orpheus' guards and the Brain's influence.
I get it that we have a problem with his treatment of Orpheus (I certainly hate it), but I find the game's handling of the dilemma, in particular, was unbalanced and inconsistent with the story's build up. They took what was a complex and compelling character, and reduced him to a generic villain, with very little we could do about it. It's incredibly disappointing.