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.
The Emperor has always asserted that he is greater than he was as a human. Furthermore, from comments and conversations, it's clear he still retains some of the feelings and memories of his past life. So while we can't be the same people we were before transforming, I think it's possible that we can be a sort of hybrid being, where biologically you're a mindflayer, but the original person is still largely there in spirit (in terms of psychic energy, I don't want to get started on souls, which is a subject that's impossible to answer). In the game, I chose to transform, and there was no difference in the way the game and the Narrator treated me. I felt like me. The Narrator mentioned that I feel myself ebbing away, but that it was possible that I can be unique and retain enough of myself, "like the Emperor". I like the idea that we can be exceptions to the norm.
