I didn't get the impression that Dr. Greer was rebelling against the national security state - on the contrary, he came across as wishing to strengthen it against the oppressive organisation. "Give it teeth" and so on. Rather than denying the war crimes of this organisation he is bringing them to our attention and suggesting a course of action to remedy the matter. Not the usual 'lock them up' policy but something with considerably less risk and a swifter outcome if we can rise beyond our vengeful nature and think of our kids' future.
Dr. Brown has spoken of a human element doing dodgy deals with hostile ETs. If this is the same element as the above organisation then there is common ground approached from different angles. It would explain how 'control ETs' would regard as significant any contract between themselves and this organisation, it being the strongest faction on the planet and its de facto representative.
ETs squabbling, abducting, hybridising - ETs in general - we can't seek to influence greatly. Or, at least, those who can are already mobilised and spreading the word among the few who are engaged. For the rest who might find that a bit beyond their reach it makes sense that we sort our own terrestrial affairs out.