There is a huge amount of constitutional jurisprudence around the notion of national security clearance and all of it rests on the idea that it is a strictly li

There is a huge amount of constitutional jurisprudence around the notion of national security clearance and all of it rests on the idea that it is a strictly limited exception to the First Amendment, generally one that is used sparingly and only when needed. This is why private citizens must volunteer to obtain security clearances. The General you speak of is presumably a volunteer who also agreed to be bound by stricter rules around classified data. The NSF does not (generally) fund classified research. They fund unclassified research at open academic Universities. If the researcher in TFA had joined a military lab and submitted to a clearance, this would be an open and shut case. He did not do anything of the sort, and so the prosecutors were forced to hunt down some workaround to achieve their desired result, then ultimately drop a groundless case.