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.
"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."