A witch hunt is almost by definition persecution of a person or persons who don't deserve it. This thread of episodes is a textbook witch hunt. The term is rightfully pejorative, and it deliberately dredges up deep negative reactions.
Parsons is a textbook Inquisitor. That term is also very pejorative. More deep negative emotions. Not only is Parsons an Inquisitor, he the worst of a Self-Righteous crusader.
There are also indications that our heroes are up against the Deep State. There are also indications the CIA is not just involved but possibly the source.
I hate crime dramas when they deal with Witch Hunts, Inquisitors and Deep State conspiracies.
The twist at the end is another joke by the writer gods. Of course any viewer knows that somehow our heroes will come through this, or at least most of them, especially Gibbs. It will be many years before Gibbs rides into the sunset. That means that his crimes, and those of the rest of his team, will once again be swept under the rug.
Framing Parsons as the self-righteous but hypocritical Inquisitor is juxtaposed against the "righteous" Gibbs. It would seem to imply that following rules and laws to the letter are being contrasted to Loyalty and Honor, i.e. The tradition of Sempra Fi, at the expense of rules. Contrasted! It is reasonable to question such unbending lack of discernment, but as a viewer I have to wonder how far the writers intend to take this thinking.