As far as I'm concerned, when I read this I had no problems with what Apple is doing. They got a memo stating that Apple is looking into it, and don't confirm/deny malware.

That's what they're supposed to do, no? This is hardly a cover up. Apple is simply reminding their support staff to not make promises they can't keep. This is a holdover till they have a solution. If their permanent solution is a cover up, that's a whole other story.