When asked about the Rove controversy Shimkus said that at the heart is whether Plame was a covert agent at the time. Shimkus said that, "no one has said she was."
The CIA obviously took the matter of Plame being identified as an operative serious enough to ask for an investigation. The Justice Department has obviously determined there is enough evidence of a crime that they are willing to jail reporters in order to get their indictment. A State Department memo to Colin Powell and potentially circulated on Air Force One indicated that the information that Ambassador Joe Wilson's wife, Valerie Plame worked for the CIA was listed as secret.
If that is not enough evidence that she was operating under cover, I don't know what it would take to convince someone.