At the time of the leak, Valerie had a day job that was no secret: she worked for Brewster-Jennings. Discount for now whether the leaker should have known that Brewster-Jennings was a CIA front -- anyone digging around in her story would learn early that she had a longtime job with a company presumed to be in the private sector. If he then learns that she, in fact, was CIA... well it's not terribly difficult to add 2+2 here.
Anyone who still clings to the possibility that she was no longer covert at the time of the outing needs to answer why she was publicly known to work for a company subsequently exposed as a CIA front. Brewster-Jennings itself was covert; any CIA operative working there would, by logical necessity, also be covert.
I think the question of whether Rove knew her undercover status is essentially answered here. If he didn't know, he had to work pretty hard not to figure it out, so much so that it would defy credulity.