Creative Speculation

The Warren Commission held an executive session in late January 1964 to discuss rumours that Oswald was a paid informant for the FBI. Their concern wasn't that the FBI had been less than forthright, their concern was that if this information was ever confirmed or made public then a genie would be out of the bottle, so to speak, and the American people would expressly reject the lone gunman story and that the powers that be (the Commission, the FBI, the CIA) would lose the ability to control the shape of the investigation.

That goes for information that Oswald had a relationship with the CIA as well, or military intelligence, or any other other agency. Point being - the official story is predicated on Oswald being a lone nut who no one could predict would just snap one day, but that story depends on false or misleading information.