I seem to be in the minority, but I think having to choose between multiple unpleasant outcomes is good. As a RL person, I prefer happily riding off into the sunset and everything coming up roses. But as a player, I like the moral quandry.
Do you trust a guy who has a history of not being trustworthy? Do you let your friend blow himself up purely to appease a goddess who dumped him? Do you make the sacrifice and turn yourself into a soulless monster? Or do you have someone else sacrifice themselves?
I'm glad you felt those parts of story worked for you. I only felt annoyance at that moment - annoyance at the writing itself not at the characters - there was no weight to the decision. Trusting the emperor was never an option for me and I was continually annoyed that the hostile relationship with The Emperor was so poorly supported by the narrative.
"I'm glad you came to your senses"
"Mmmm, no, I'm just upset you didn't die when I stabbed the illusion you constructed"
I dunno what I see in Emps. I'm someone who struggles with social stuff and empathy so I suppose because the Emperor is different, I identify with him on a level that others don't.
I get that. I've had lots of discussions with fans of The Emperor and that does seem to a common thread. They see the emperor as 'queer' in the widest possible sense. As someone neurotypical who struggles with social relations, as someone gay who is afraid to show their true face to the world . . .
But, for me, if I were to choose a real world analogue for the brain eating space squid I would choose: abusive romantic partner. The Emperor lies, gaslights and manipulates for his own ends; he protects and provides *until* you disagree with him and then you see his true face. And while the alignment grid and real world morality are entirely different beasts if I were to judge him by the morality of our world I would judge him as someone who treats people as ends and not means unto themselves and so objectionable by the standards of Faerun and the real world. (and that's before we talk about the murder and organized crime)
Indeed it angers me all the more at the start of the chapter 3 railroad moment that he gets to frame our objections to him as if they were objections to physical form and not the fact that he's enslaving someone's mind . . .
I could go on a length but I don't want your point to get lost:
In any case, I would like an option that allows the githyanki to be free from Vlaakith, without someone needing to transform into a mind flayer.
I agree completely. And while I would prefer a substantive rewrite your suggestion is a good one

You should send it to the devs!