The attitude of the FBI towards diplomacy portrayed in the story is pretty alarming. I generally have a positive view on the Obama administration, but their pursuit of "leaks" post Wikileaks & Snowden is deeply upsetting to me.
Suppose the US government database says the US drone program in Pakistan is classified top secret and she did not have official permission to speak about it. Except that everyone who is anyone knows about it. So the difference between how the US wants something to be classified and how secret it actually is allows FBI to say she talked about things without permission, when her bosses in State know she didn't tell anyone anything they didn't already know.
To me this whole SNAFU boils down to the two FBI agents assigned to the case not doing due diligence in their investigation.
The tl;dr is basically this: administrations before Obama definitely wanted to crack down on whistleblowers, but were limited in their ability to do so. The fact that whistleblowing related arrests/convictions have increased under Pres. Obama is largely due to the fact that we can track people and information much more thoroughly than was previously possible. In the past, you may know who had access to any one piece of information (that leaked) but you would be hard pressed to identify communication channels and specific, time-logged access, etc. Investigational tools have improved so more convictions happen.
This doesn't address the civil liberties expectations/promises of Pres. Obama, but it's one factor at play.