As for the Emperor's rationale, that just reinforces the point: if thinking like a mind flayer is sufficiently different from thinking like you, then you're no longer you after the transformation. Instead of you, there's just a mind flayer who happens to have some of your memories. Just this happened to the Emperor, which you can deduce from the documents you find and which is made clear right there when he wants to consume Orpheus' brain. So you really become the enemy, mind and body, and whoever is the one taking this on themselves will no longer exist.
Excatly. And what also stuck in my mind was a book you find at the Emperor's layer. It describes what to do when you are under the influence of mind flayer manipulation. Not only was it the perfect foreshadowing of what would happen if you tell the Emperor "No" on the Orpheus matter. But it also serves as something you don't want to become (unless you're aiming for it specifically in your play-through).
The book tells you to never trust a mind flayer. And if you're happen to work on a common goal together, the mind flayer will drop you as soon as you're no longer useful to them. The advice you get is to build strong relationships with your allies instead.
So, unless my character is somehow special, I would now treat my allies this way and discard them when I no longer need them, if I decide to become a mind flayer.
