Does the military have the full list of CIA operatives stashed

I doubt they have some kind of master list. The reason being, theres no purpose to have one and if such a list did exist, it would be a huge liability. I would guess theres a lot of compartmentalization for security's sake.

Are you talking some Cerberus from Mass Effect defect where they are trying to help their old allies but use questionable methods or full turncoat?

>>33080533
If it turns out something like South Korean situation where people who actually call the shots are some shadowy moguls.

>>33080468
>Sir, we should make a list of CIA operatives in case CIA goes rogue
>Brillant idea, have multiple thousand dollars reward for this idea
>Can i get paid in rubles?

No. You trust that if they do go rogue, there exists enough of a paper trail, infastructure and clerks to compile that list.
Keeping a actual complete list in itself would be braindead and retarded.