The best way to screw her over would be to abandon her behind enemy lines, since then their hands would be clean of her murder. Recovering her wristcomp from her at that point would be an outrageous risk for them, and if she died before getting back then the wristcomp would do her no good anyway. The same goes for if they simply decided to shoot her in the back of the head, once she's dead all her problems go away.

Also since her wristcomp is part of her standard gear they'd have no reason to take it from her before she left for the mission, unless they want to come out and blatantly admit what they're doing is wrong.