What the CIA should have done is have phones which impersonate actual, "normal" phones when necessary and send messages which resemble normal messages. Not "PIZZA!" but whatever the local people send, e.g. "miss u". There could be a challenge-response that is not deterministic, e.g. "are we still on for tomorrow?" "looking forward to it" and then some normal sounding conversation (of course, tomorrow wouldn't be the day they would meet).
The key is to impersonate enough phones (tunneling over a trusted subset of the network) or use a network that won't identify the endpoints. The former is much easier.