The chances of a small plane doing terrible damage is small
And apparently the guy made it clear he was a wackjob pretty quickly.
Unless the plane was loaded with gas or germs or a tactical nuke, it was not much of a threat.
The fact is, the vulnerability that exists is deep seated in the structure of the world's culture. Blowing the plane up or shooting it down could have spread a lot of debris and fire over a large area.
I don't envy the people who have to make these calls.
Ed