I read Perfect State when it came out. Reading your annotations and the deleted scene has jogged my memory. Honestly, I never made the connection that Sophie was Melhi for all intents and purposes. I believed Melhi's facade and thought he was simply a crazed do-no-gooder (I totally forgot that the Wode mentioned Melhi's gender).
Reading the deleted scene makes things alot clearer though. I was chatting with a friend about the deleted scene and we agreed that we're glad it was omitted. It smelled too much of the Matrix and, worse, it cheapened Kai's betrayal. That is, "Sophie" didn't really die. The person that Kai found attractive due to her outlook and personality was in fact not a creation on Melhi's part to simply hurt Kai but was Melhi being her honest self (I imagine it's much easier to just be yourself then construct a person as realistic as Sophie). Melhi being Sophie undoes the reversal of Sophie being a robot. Shadows of Self spoiler: It'd be like if at the end, after the Lessie/Paalm reveal, we find out it's really a different Kandra after all.
Regardless, the deleted scene interests me and leaves me wanting a sequel.
Edit: More thoughts. I appreciate understanding Melhi's motivation for how and why she does what she does. I don't think I picked up on that. Again, I took Melhi at face-value. I would say that Melhi is pretty selfish though. She feels she knows best for everyone else. That it's better for others to feel the same way about being a brain in a jar as she does. This is obviously an opinion though as any revolutionary can be viewed as a traitor.
I think your analysis is spot on, both about what the scene does to the story, and Melhi's character. I would call her selfish, but in an approaching self-aware way.
Either way, I'm glad to have this out there, but--though I go back and forth on it--I'm mostly glad that I left it out of the official release of the story.