He knows the CIA did something illegal, but is protecting them. If a mafia member shoots an innocent man, and a judge says "I feel bad for the guy, but the mafia is good for this city, so no can do; yunz are screwed!" it's fairly obvious what's happening.
He's preventing criminals from feeling the consequences of the law because of perceived value.
No, he's upholding the law, whether he agrees with it or not, which is his job. A judge's job is to adjudicate based on the law and he adjudicated that states secrets was lawfully invoked.
He's preventing criminals from feeling the consequences of the law because of perceived value.