Hmm. On the one hand, the government seems to be looking for contractor assistance in collecting malware; and on the other hand, they seem to be attempting to snuff out non-governmental security researchers. Could it be the government is seeking a monopoly on the collection, research, mitigation (and potential use) of malware? Now THAT's a chilling prospect in an era of rising "Big Brother" concerns...
However, in this era of incompetent and massive governmental bureaucracy bent on enhancing its own power and role, it's more likely their left hand has no real clue what their right hand is doing. And even less 'clue' about the Constitutional legality of any of it...