He is not the only ex-CIA who has been working behind the scenes. Watch the movie "The Recruit" about the CIA. They do not necessarily tell the agents doing bad things, that they are in fact doing bad things. There is a lot of secrecy and double crossing and TESTING OF AGENTS and if necessary blackmailing of agents.
Jim Morisson had a great gig because he was pretty much free to have a wild time and set an example for a generation to have a wild time. So he did it and sometime while dropping acid, he had a flash of insight and figured it all out. If he talked to handlers about it, they may have attempted to have him killed.
Maybe someday the story will come out.