I'm going to play devil's advocate here and say that in this case, and for purely pragmatic reasons, a kill mission was a much cleaner and faster way to deal with him. Yes, in theory, you're right - everyone should get a day in court.
In practical terms? You can put a bullet in his head. Terrorist groups will get riled up, then the dust will settle and it'll be anthrax-sniffing-business as usual for them.
Or you can go by the book and take him prisoner. Have a show trial that will drag on for months, during which time the media would be doing a great job at helping to heat the situation up and up as the various terrorist cells activate and start sending messages of their own. In the end it would have likely resulted in more random civilian killings. Of course, I can't prove it, but I think it's a reasonable hypothesis.
By the book is by the book, of course. It's not always wise, however. In this case, you have a man who wouldn't have been rehabilitated anyway. Instead he'd become a reason for someone to abduct a plane to demand his release.
And honestly? Steal a million bucks, run over someone drunk, sure you get your day in court. Kill so many random civilians? Bullet to the head, good riddance.