CIA had no control over shoot/no shoot, they could only advise, as was mentioned. The Peruvian pilot also gave warnings on the international GUARD channel, but apparently the guy at the controls of the seaplane decided that listening to someone or something else on another frequency was more important.
Aircraft have two or more radios for a reason. You always keep one tuned to 121.5MHz not only because that’s the international distress frequency but because that’s the channel that MEN WITH GUNS AND MISSILES THAT CAN BLOW YOU OUT OF THE SKY will use when they want to talk to you.