Gibson wrote an excellent article on the creation of the Warren Commission (included in the book The Assassinations, edited by Jim DiEugenio and Lisa Pease). This book continues his detailed analysis of the Warren Commission and the mainstream media's involvement in the cover-up. Gibson concludes that the Eastern Establishment (not anyone in "The Government") was responsible for JFK's death, with John McCloy, Allen Dulles, Dean Acheson, Eugene Rostow, Joseph Alsop, and James Reston at least being the key people involved in the cover-up.
"In Kennedy's time the Establishment, including many people associated with McCloy, was preparing to launch a new effort to convince people that progress had become near impossible due to resource scarcity, overpopulation, and the destructive nature of large scale, modern industry. First called the new conservationism, it later became known as environmentalism. Kennedy was opposed to this sort of political, Malthusian environmentalism. He showed no signs of accepting the pessimism associated with this movement and he was on record stating his optimism about the potentials of modern science and technology to overcome problems such as those related to resources."
I think this theory is as vague as most of the theories put forward by various researchers. Part of the problem is the way we toss around terms like "Eastern Establishment," "military-industrial complex," "organized crime," etc. without realizing how interconnected they are, and how many players have been members of all these groups and more. There is no way to draw neat dividing lines between them.
Also, this book was written before the revelations about Operation Northwoods, which frankly has reshaped my thinking about the assassination. There is also little discussion of the mysteries of Oswald's alleged trip to Mexico City. Personally, I think the Eastern Establishment would have been more likely to tamper with Kennedy's medications or cause him to have an "accident," rather than blow his brains out in public and pin the blame on a pro-Castro activist.