It shouldn't fly. That's why in my original post NSA was listed dead last as a probable data source, far below normal federal law enforcement means (such as administrative subpoenas). Even those were far less likely than simpler explanations.
As far as fingerprints, I agree the interface available to IAFIS database end-users may be restrictive. However, due to the highly aggregated nature of the data, and the fact it's maintained for law enforcement by law enforcement (namely the FBI), people expect it to be available to a myriad of government agencies (which it is).
With Facebook private messages, you expect only Facebook employees (or partners) to have access, or in special cases government via warrant or subpoena. Major tech companies took a fairly large PR hit following the news of NSA having wholesale access to their systems, precisely because of these expectations.
If the headline was instead "FBI grants NSA full unrestricted IAFIS access." nobody would bat an eye, because it's expected. The FBI is heavily involved in national security affairs themselves.
My point was, the sensitivity of the collection method is a major factor in determining the classification level of the data. The PRISM leak is a prime example of this.