I'm not surprised by this to be honest. Does it make it right for Disney to do this if he went about it correctly to get the permissions? No. That was a dick move on their part.
Though to my mind if he had those kinds of resources and creativity, why bother making a Star Wars fan film at all? Why not make your own original content and have ownership/ control over everything about it?
You watch. This will set a precedent. Not long from now they will ban fan films altogether. They may even go after prop, model, and costume sights like theRPF. It wouldn't surprise me at all. If you think it's bad now, it's only going to get worse. I know this sounds extreme, but they could very well go after all kinds of people to protect their IP.
Adam Savage even said on one of his podcasts that a friend of his that still works at ILM or Lucasfilm knows everyone who is making and selling Star Wars stuff. It wouldn't shock me in the least.