Great analysis!

The Emperor getting angry at you for going after Raphael has bugged me on both Tav and Urge. Raphael wants the crown... not just a stone, but the whole crown that controls the brain. And he's not going to stop at anything.
The story makes you believe that the Emperor is always a few steps ahead when it comes to thinking about possible outcomes. That's why an illithid can only control the stones at the end. Because, like the elder brain, they think adead. Yet when it comes to Raphael, it seems that such a dangerous person being after the crown should not be meddled with.
The Orphic Hammer is the best thing Raphael has to offer. The most logic reasoning, imo, would be for the Emperor to ask you to steal it and give it to him. Especially when you play (evil) Dark Urge. Because what are we going to do with the hammer? Free Orpheus out of the kindness of our hearts? I don't think so. Even playing Urge who is trying to be good, the Orpheus dilemma doesn't feel like a priority. Simply because figuring out your mush brain and dealing with Orin and Gortash seem a lot more important. Raphael, however, has been on my mind because he's basically after the same thing we want. The Emperor should be able to see this, with him being constantly in our heads.