If your reaction to this news is "something more is going on here" then I think you need to take a step back and re-calibrate your bullshit detector.
Could there be more to this than meets the eye? Yeah. There could also be more to the moon landing than meets the eye.
It seems to me we all must, in our attempt to be rational, do our best to check our biases. For a lot of people on hackernews, that means second guessing your immediate "NSA cover-up" reaction to any item of news involving the NSA.
I think the most likely scenario here is that the government is making an example of this man. I don't think that's right, and I hope he gets off with as slight a punishment as possible, but it is a fact that governments have secrets and have enacted laws in order to try to keep them.