Well, emotions aren't the same as thoughts. He's firm against mind control (for understandable reasons I may add), but they keep control of their own thoughts.
I can understand the concerns, but I hope it won't be a big problem. From what I understood is that in PvP the GM has the final say in fights and the emotions she'll send should be more seen as a distraction rather than full outright control of their feelings. The idea I had for controlling the loyalty would be mostly in fights with NPC soldiers. From what I read they patrol in groups of four, Natasha could make one of those 4 feel very uncomfortable between his comrades and end up attacking them or have them temporarily switch allignment, but while she's performing this attack she'd need all her concentration just keep his emotions under her influence. Versus ordinary player characters that particular ability will be ineffective. (I hope to have made that clear with her weaknesses.) It'd probably actually be faster if she just gave the guy a headshot.
In a way it works like a mutant who can create distracting illusions and make other characters see things that aren't there. Natasha's empathic ability should be seen like that, except now that she makes others feel things that they aren't really feeling, and thus ends up distracting them in the process. It's more a distraction than control.
It's a bit hard for me to put it under words, but I can assure you that I won't make abuse of her gifts. I actually think that her empathy will mostly be used to relieve the pain that injured characters feel while she works on them with her healing touch.
My description is still a work in progress though and perhaps I should clarify that part of her abilities better. I also don't have an issue with dropping the part where she makes others feel so loyal to her that they'd temporarily switch sides. It's only useful on the grunt soldiers anyway. (It's a bit like how Jedi mind tricks work, those work on Storm Troopers, but not on Darth Vader, or even their squad commanders.)