I'm sure we aren't getting the full picture.
The FBI probably wants to send him to Guantanamo and take his rectum.
However they haven't done that.
So either the FBI doesn't have a case, or they're trying to build one.
Or they are scared of a possible backlash to this by the public (yeah right), or by others/terrorists taking advantage of this flaw.
They probably want to avoid another Snowden incident.