I read it the same way, and I don't see how one would read it any other way? Removing the qualifiers -

"If El-Masri's allegations are true [..], then all fair-minded people[..], must also agree that El-Masri has suffered injuries as a result of our country's mistake and deserves a remedy."

The quote there is just the recognition by him that the CIA committed crimes. The context of the rest of the decision still finding for the CIA is the half that you're missing.

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.

The Constitution comes before every other law, and allowing the Constitution to be waived is against his job.