I don't think anyone is saying that Junk is her counter since it is still pretty hard to actually kill her that way. It's mainly that Junkrat is not a complete sitting duck against a Pharah now and finally has some sort of teeth against her.
On live, it's rarely worth playing him if the other team has a Pharah unless you're fighting in a tight space. This will make him still a viable pick since he can realistically be a danger to her now, even though he's still not the ideal option for addressing her.
But maybe I'm wrong.