I think it originates from the same dark place as "Roger".
From what I have been told about those two phrases is that it orgininates from the good old morse key, coupled with the old phonetic alfabet.
The letter C where used to confirm a message in morse key, and as the radio operators moved from morse to voice, the took the C with them and therefore said Charlie Charlie.
This is what I have been told, and it makes more sence than most, I think.
Be well
Fresca