[0]: https://www.history.com/news/us-overthrow-foreign-government...
It's really not that hard to understand.
We pay the CIA to forward American interests. Most of their actions, even the most nefarious ones I'm aware of, have a somewhat believable rationale as to how they fit into that overall priority - often extremely imperfectly in both ends and in means. So if someone could put forth a theory for how assassinating JFK would benefit CIA or the US then sure. But largely the CIA implication is just "big shadowy CIA is responsible for all the unexplainables."
There are plenty of theories where the CIA benefit from his assassination.
> Shortly before Hunt's death in 2007, he authored an autobiography which implicated Lyndon B. Johnson in the assassination, suggesting that Johnson had orchestrated the killing with the help of CIA agents who had been angered by Kennedy's actions as president. [0]
Some think he was removed due to his immanent withdrawal from Vietnam. [1]
Nonetheless, if you are the head of an organization that deposes governments by assassination, is it really _that_ far fetched to think you are above the law and would use the tools and your disposal and experience to dispatch anyone in your way?
[0]: https://en.wikipedia.org/wiki/CIA_Kennedy_assassination_cons... [1]: https://www.bostonreview.net/articles/galbraith-exit-strateg...
Edit: Did you read the "JFK decided to withdraw" link? He allegedly decided to withdraw 1000 of 17,000 Americans in Vietnam. This one step forward two steps back military strategy is par for the course for the duration of the Vietnam War. Doesn't substantiate at all why CIA would be so upset about it as to assassinate POTUS. Per your own link, it was a minor enough move that they didn't feel the need even to consult or notify South Vietnamese President Diem.
There are a lot of examples in history when this was not a problem.
> It's really not that hard to understand.
It is. When all their actions show something else.
> We pay the CIA to forward American interests.
Yes. But your's "American interests" might not be CIA's "American interests".
~ Famous last words.
But then a decade later you have the Church Committee directly investigating abuses from all of these agencies, which results in President Ford issuing a congressional order that explicitly forbids U.S. involvement in assassinations (going further than what people claim Kennedy was trying to do), and these agencies do...nothing.
Unstable people are easily discredited. The CIA literally coined the term "conspiracy theory" in response to people not trusting the narrative as a means to preemptively discredit any unwanted suspicions. That's totally something a legitimate organization would do.
And stating that Kennedy would "curtail their operations somewhat" is a gross understatement. Kennedy was costing the Dulles brothers lots of money. Bay of Pigs, literally averting the takeover of a country that the CIA attempted to kick into motion- that's a bit more than curtailing somewhat.
And the Church committee was toothless. No legislation resulted from it- simply an executive order. The Church committee is also credibly accused of limiting the scope of it's inquiry in order to protect the CIA. And of course the agencies did nothing - they didn't need to do anything, they continue to operate without real oversight to this day. Spying on the Senate, then lying to Congress...zero repercussions. The Bushes, Clinton- all presidents that had interesting CIA connections.
The biggest issue they have now is competing with other Intel agencies, foreign and domestic.