I completely agree. It's one of the things that stuck with me after beating the game and left me feeling a little let down by the ending.
Big spoilers for an ending route and ending:
If you get the hammer from house of hope, reject the emperor and save Oroheus several weird things play out:
1. The emperor tells you that Orpheus will try to kill them because of his hatred for mind flayers, which is fine.
2. The emperor decides to join the elder brain (the thing that his whole life's mission has been to destroy) and fight you instead (wtf?)
3. Orpehus is free and immediately suggests turning into a mind flayer - which is exactly what we just rejected the emperor for.
4. If you continue to reject the idea Orpheus just magically turns himself into a mind flayer - with no tadpole (also wtf?)
It would have made more sense if Orpheus had praised you for rejecting the tadpole and instead joined you as Orpheus the monk and helped you beat the game without any of the mind flayer powers. The mind flayer powers aren't really that useful in the end if you haven't been leveling them anyway. Another thing is that if Lae'zel is with you she takes over Orpheus' work for him, they could still just write some excuse for this that would make way more sense than Orpheus becoming a mind flayer, like Orpheus is tired and doesn't want to do it anymore, or he dies for some other reason.