To be fair, the NSA outcry was largely over the scale of the monitoring and the lack of warrants. However that doesn't mean that (other) government organisations couldn't approach Facebook with a warrant and request specific data, such as private messages from a suspect.

Assuming for the moment that this story did happen exactly as we're lead to believe (and I'm only making that assumption for the sake of playing devils advocate - I'm firmly on the fence with this story due to how sketchy the details are), then it would be very easy for the NSA to cover up how they had such data: "We'd been investigating her for a few weeks - here's a warrant"