Yes, it's the fact that people are being killed to repair her face, or so it seems, that's really disturbing.

Two things I just thought of on the double agent theory: she's the one who suggests that they try using the staffs to lure the FM out, and why would she do that otherwise? The other is that there are a lot of situations where Peter goes off to do one thing, and Nightingale and Lesley do something else together. Plenty of opportunity to plan things out, if Nightingale was in on it.