Yeah, that was harsh. Can't really blame the guy, though, since at that point I think he half-expected he was going to die (except of course that no one ever kills their enemies in EMH).
I did wonder if she had something to do with how quickly he was suddenly out of his cell...
I also wondered about the fight in (I think) Gamma World where he got the other hand. I felt kind of bad but I figured that for some reason she let him ;)