You can't stop the Emperor from being stupid, but you can
prevent Orpheus or any party member from becoming a mindflayer after freeing him
by bringing Lae'Zel and a bomb-enthusiast Gale with you to the scenes and following an incredibly specific dialogue path.
The basic rundown is
agree with the Emperor to turn someone into a tadpole, talk to Lae'Zel about not killing Orpheus and Gale about definitely blowing up, then accept the tadpole but change your mind after it's given to you, then talk to Orpheus about the Gale bomb. The only way to convince Orpheus not to transform is if you have the final tadpole and promise to use it if Gale bomb fails.
It's not what you want, but it's the most you can do to mitigate the arbitrary nature of the ultimatums the ending tries to force on you.
Honestly I don't think either of those are really poor decisions from a story standpoint. To me it makes perfect sense why the emperor doesn't stick around. It seems entirely in his character and from his perspective it's a totally reasonable, sound decision. And with the brain, I think the mistake there is having us roll at all, not that we can't do what we try to do.
The reason I don't agree with this about the Emperor is because he doesn't just leave. His choice of where to go throws off his entire characterization which, given he was adapted from another role in the plot entirely to fill Daisy's shoes, is shockingly solid otherwise. Rather than calling into question his trustworthiness or conviction in a narratively satisfying way like for instance just running away in the Astral Plane because he doesn't think we can win, you're left with "so he was full of shit all along." It likely ended up this way because it made sense for Daisy and they just didn't adjust it enough.
