Poor Ruth, but I agree, Emperor + Agent story lines would lead to mind control of some kind. Especially after Lord Scourge's betrayal, the Emperor would not make the same mistake (or he'd try not to) with the new Wrath.
Ruth does not seem to be totally aware of the difference between her Emperor-mission self and her normal self though she did have that kind of dirty feeling the first couple times. I remember in RMC Quinn noticed but never said much about it. I wonder if Wynston will be different.