That rumor has been around since the beginning. The story was that Wilson was fond of telling people at parties and other gatherings that his wife was a CIA operative.
Novak could have been at one of those gatherings, or almost anyone in DC could have told Novak about her job, and he might have pursued the story from that side. Novak might not be telling because he's protecting a source that he uses for entirely unrelated stories.
Anyway, her job was not a secret any more than is the fact that the Press is anti-Bush.
Wilson had written about his wife's job in a previous book or article he'd published.