My theory? That was just part of his interrogation. Think about it: he doesn't throw them out of the plane because he would need to explain where they went mid-flight, but he pretends to shoot them and goes through this whole "first one to talk gets to stay on my plane" spiel because he wants to threaten them with death even though he can't. The flight plan had all three prisoners, the agency couldn't investigate since they had no official access there, and the local investigators are incompetent and can't be trusted so the agency gets the wrong number of bodies.