This seems pretty silly to me.  It conflates RANK with STATUS.  The better analogy, I think, would be to a DEA or FBI undercover agent.  When the agent is on the undercover assignment, he/she is "covert"; when the agency ends the U/C assignment and transfers the agent (often to a supervisory position), the agent is no longer covert, even though aspects of the former assignment remain closely guarded.  

Obviously, when an undercover agent moves onto new, non-undercover responsibilities, that does not mean all entanglements of the covert assignment are over.  If, for example, there were classified aspects of the assignment (e.g., the agent's cover was a sham corporation that the agency is still using for undercover purposes), or if the agent, while covert, reported information that is still regarded as sensitive or classified intelligence, all that remains closely guarded (perhaps even classified).  So, to that extent, it can still be said that the agent has "covert" responsibilities. 

BUT, that doesn't mean his or her day-to-day responsibilities are any longer covert.  The agent, for example, walks in and out of headquarters everyday, like hundreds of other people, because there is no longer any imperative to conceal his/her connection to the agency.

We don't know all the facts necessary to render a definitive judgment, but it sure seems like Mrs. Wilson is using the continuing sensitivity of facts about her formerly covert STATUS to suggest, misleadingly, that she continued to have a covert RANK once she returned back home and was assigned to headquarters — where a zillion people a day saw her walk in and out of CIA and the Agency was obviously not trying to conceal the fact that she worked there.