The news report I saw suggested that he did not stop when commanded to by the air marshalls.

I have some sympathy with those guys - if someone seeems to be behaving in a suspicious manner it is their job to deal with the situation. I suppose it's possible that, concentrating on the guy running toward them, they may not have heard what his wife was saying the other end of the plane. However, I wonder if they had orders to shoot to kill, rather than to disable a suspect, and, now that the whole story is known, I wonder how they feel.

This sounds like a similar event to the shooting of the guy on the underground in London after the bombings. As in that incident there will be a number of versions of the event and lots of theories flying around. Whether we ever hear the real facts is debateable.