Well, he never really ruled that it is illegal per se. That Washington Post article is terribly misleading. The judge only ruled that the FWS failed to follow the law when it enacted six new rules allowing or expanding hunting on certain refuges because it failed to have an Environmental Impact Study done before it finalized the rules.
The judge declined to declare the rules void, pending supplemental briefing by the parties on possible solutions.
So, the rules may stay in place or be replaced. All the agency has to do is complete EIS, and the EIS's have to show that hunting will not harm the environment. Of course, in reality that makes passing such rules more difficult, expensive, and time consuming. But it certainly doesn't mean that hunting on refuges is illegal.
Of course, this is a not-even-veiled attempt to eventually end hunting on such refuges by making it economically burdensome for the agency to allow or expand it. The solution would be a clarification of the law that the FWS isn't required to complete EIS's. That could happen by legislation or on appeal, and I'm sure this is being appealed.