Which is why I suspect it doesn't really matter which way they were looking on 9/11.
I suspect you are correct. As an Air Traffic Controller of over 20 years, my perception of what could have been done with the WTC aircraft is grim. In the time it takes to humanly recognize the nature of an incident like this, it is over. The idea to shoot down any aircraft that has a communication failure, loses its transponder or behaves erratically for a few minutes would mean the downing of a dozen aircraft every day.
If NORAD was set up to monitor all the daily flights for erratic behavior, it would have a staff nearly as large as the FAA, and the results would be the same or worse. Worse being the complications that arise with overlapping duties or missions.
The true cure for this, sadly, is removal of the privilege (or right) for private citizens to fly aircraft. Id est, fewer planes means closer monitoring and restrictions on routes and proceedures. This could be coupled with mandatory public motorized mass transportation, etc., etc. In short, how far do we restrict our freedoms to be "absolutely" safe?