But what if the person was unconscious or in VR? They'd be unable to resist (Well, I guess if in VR they could try to hack their own commlink to regain control

).
The OP's situation was one where he'd voluntarilly let his agent act as the brain for his skillwires while he was off floating around in VR. So the only thing we're left with now is trying to determine the degree of control over one's body the skillwire system has.
We should look at the type of activities the skillwire system allows the user to do, and determine if we can explain them away with "subconscious memory" and "theoretical knowledge".
My thoughts on Muscle Replacement:
"Muscle Replacement: Implanted, vat-grown synthetic
muscles replace the user’s own." pg. 334
RAW imply that all of the user's muscles are replaced. If the Muscle Replacement was a subscriber to the character's commlink, then I don't see how an Agent with an appropriate autosoft wouldn't be able to control it (as long as the character didn't resist, or was incapable of resisting). Yeah, that's scary.
Has anyone explored the possibility of rendering a person braindead, and then having an agent control the body from then on?