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.
From a story standpoint, this forces a hard decision, which is something I usually like.
And it�s totally reasonable that you can�t reason with the Emperor as a non-Illithid. It�s clear at that point that this is similar to a child trying to talk with an adult about a math problem.
But after transformation, I would love to have an option to say �Orpheus won�t harm you. Our friends will make sure of that. If he tries, I will assimilate him. We trusted you with our lives again and again. Now it is time for you to trust us. We are not Ansur. We respect your wish to live.�
And if the friendship to your friends is high enough (maximum?) even Lae�zel will stand with you (since she also lets you assimilate Orpheus if you convince her).
And it could actually add another hard choice: if you have a companion, the Emperor could ask you: �If I take this risk, will you leave (name of companion) and join me after we defeat the brain?�
It is clear that that�s something he wishes for (�you are exquisite!�), so that�s additional leverage. And it preserves the plot aspect of forcing a hard choice just before the end.
(I read that Omeluun reveals elsewhere that his ring of protection doesn�t actually protect him, but that he just gave it to you to make you feel better, so it doesn�t provide a way to give the Emperor safety against Orpheus)
