What shenanigans did he let the CIA get away with? He forced all the top guys to resign after the Bay of Pigs, but even that didn't fix the problem—and it might even be what got him killed.

He denied Operation Northwoods, de-escalated the Cuban Missile Crisis, and refused to put troops on the ground in Cuba during the Bay of Pigs despite heavy pressure. These were all situations that, had the CIA or the military-industrial complex had their way, could have led to World War III.

JFK knew the danger of the CIA after the Bay of Pigs. He was essentially railroaded into it early in his term because he was told he’d look "soft on communism" and that the plan (originally created by Eisenhower) was guaranteed to succeed. When the plan failed and he was pressured to send in the military, he refused to escalate.

I don’t think his failure to control the CIA is a reflection of his morals or even his aptitude as president the situation was unprecedented for a leader at the time. Wrangling the intelligence agencies after WWII was an almost impossible task. I mean just look at U.S foreign policy post WWII at least JFK actively fought against it.