Well, he does not need her permission to write fan fic. He only needs her permission to publish it, which she will not give. If she let him publish his fan fic, then she'd have to let everyone try and get their fan fic published. Because although his fan fic has a cool website and it got a lot of Internet publicity, it's still just fan fic.
JKR has no plans on letting people publish their fan fic, which makes sense. Harry Potter was her idea, so other people shouldn't make money off of it. As a fan fic writer, I understand this and agree with it. I'm perfectly content just to write for the fun of it. My reason for writing fan fic is so that I can further my HP obsession.