If Ruth was a conspirator, it might have been just as an informer. The CIA director and agency as a whole may have had nothing to do with the assassination and may not have been aware exactly who might be an informant to the conspirator group of persons.
And it’s doubtful that CIA would eliminate one of their own without definite proof of being a mole or counterspy.
And a conspirator group sharing the same resolution that it was a necessary act to eliminate JFK probably also took some kind of oath never to reveal the truth.
For what purpose? What did she and Michael get out of such an act? Ruth Paine was (I guess still is) a liberal Democrat, was pro-Kennedy, and not the type of person as a self-professed Quaker pacifist to join with essentially a far right wing putsch or treason. Again: treason. I don't think she would conspire with anyone to murder another person much less JFK.
If you read Thomas Mallon's book on her, "Mrs. Paine's Garage", you'll see that she talked about going to Central America in the 1980s as part of a Quaker relief organization to help victims of the Contra war (she was accused by one person of working for the CIA at the time). She said she was disgusted with what the CIA was doing in Nicaragua and protested by withholding 25% of her taxes. That doesn't sound like a person who would mindlessly support the CIA.
Ruth Paine is simply not, for me, the type of person - either politically or emotionally or psychologically - who'd want to kill JFK or be part of a conspiracy to do so. And then keep it quiet? Again, why? Unless one thinks she's pretending to hold these views all of these years. She's sort of a female Herbert Philbrick but in this case a right wing type. If not then why go along with this?