Do you think that she may have been "on the books" in the Human Resources office of CIA as covert, purely for pay differential purposes?
Let her produce the SF50 (or CIA equivalent).
No. Given her position, she has to deal with other USG agencies. I am sure that many outside the CIA knew her name. The fact that she didn't even bother to change her name indicates to me that she was not covert in the real meaning of the word.