Let's place the blame where it lies -- with this idiot judge. If a plaintiff has a legitimate case, and the goverment has a legitimate reason for secrecy, then it's the job of the judge to navigate these waters so justice is done. The judge has a ton of tools at his disposal. He can exclude certain evidence. He can review the evidence himself, which is probably what he would be doing in a bench trial anyway. He can give an indication of how he is likely to rule, knowing what he knows, and push the parties to settle. He can tell litigants that their chances would be better if they used lawyers who were cleared to have classified information. There are hundreds of things he can do, and he is required to do them, because it's his damn job.
We give way too much deference to federal judges.