Her position as a federal lackey, er, I mean agent, has absolutely nothing to do with the hypo. In VA, (and most states), your wife, or any citizen for that matter, can use deadly force to repel deadly force or what she reasonably perceives as deadly force, period. It is assumed, in the hypo, that escape is not feasible. In the home, she can use it against a trespasser so long as she reasonably believes the person is going to threaten at least serious bodily injury to her and/or other family members.
Ever take a look at Texas' deadly force laws? Sheeeeeit; they can cap a trespasser, at night, who is stealing a garden hose! That's right, they can use it for property theft at night.
Rape, carjacking etc.? Certainly that was a rhetorical question. Of course she can.