I realize that Ray McGovern is trying to imagine how Russian analysts might interpret the conflicts within the USG, but I have never bought into the idea that the CIA played any role in JFK's assassination, nor that subsequent presidents ever had any reason to fear plots from within the security apparatus. The kind of people who are allowed to become president already share the values of that apparatus, however much they may occasionally disagree on tactics. There is, for example, zero evidence that Obama does not share the more bluntly spoken Dunford's view that Russia is an "existential threat" to the U.S. Even Bernie Sanders shares the standard view of opposing Russia and supporting Israel and Saudi ArabIa - even though none of his dreams are possible when military spending consumes so much of the federal budget.
This is not to say that there are not people within the security apparatus who are capable of any crime, even assassinating a president, but their disagreements with presidents are never so great that they would take that kind of enormous risk.