It's very important not to look at an event in hindsight when judging the decisions made during it. Prior to 9/11, every hijacked airliner ever had either been held for ransom, used to reach a destination other than its intended one, or in a few cases directly robbed itself and then released.
The wholesale killing of passengers and crew was rare, destruction of the aircraft unheard of, much less destruction of the aircraft by flying it into a building. No airliner had ever hit a large building, intentionally or otherwise.
Unprecedented events always look very, very different from the other side. Just because unprecedented action could have stopped the event doesn't mean the nature of the event was clear in time to take that action. Especially considering that unprecedented action would have meant killing US citizens in domestic air space over populated cities.
The irony here being, had they stopped the attacks by taking that unprecedented action, they've also made it much harder to prove the event was unprecedented and called for such a response. Again, applying hindsight to the opposite outcome will just create an equal-but-opposite conspiracy theory when by immediate appearances the Pentagon responded to a hostage situation by blowing up the victims.