Wilson calls Novak and more or less threatens him and says - Shut up about my wife. Novak remembers "the friend"....does a little research (Dem Contribution List) and publishes his article. He used the words "CIA Operative" to smoke Wilson out...and he did just that. What Novak meant by "Operative" was Dem Operative. Wilson took it to be CIA "Undercover Agent".
My best guess is that Novak knew Valerie from his DC social contacts...before she married Wilson...when she was just Plame old Valerie. It was hardly a "secret" marriage.
I think it was more to do with the CIA being mad about Cheney and the WH "interfering" in the CIA's domain.
BTW: No one ever mentions that Wilson was still married when he began dating Plame. It is only relevant because it says something about their characters.