BB, guess what? There is no sure way for Chug "to protect his Society from Terrorists". You just do your best, mainly with intelligence, by infiltrating, by using brains rather than brawn. I doubt very much if any plan involving extraordinary rendition (a glorious word with pseudo legal implications, when it is only really good old fashioned kidnapping) would have much facility. You do what you do with all bad people; investigate, arrest, and prosecute them. If they confess and plead guilty easy peasy, if not then do your work assiduously lest they slip the net.
As to Khalid Shaikh Mohammed, I understood that he had confessed, so what's the problem? Oh, he only confessed under torture? Ah...