First, "NORDO" stands for "No radio", not "no transponder". FAR 91.185 deals with loss of communications procedures, both from the pilot's and ATC controller's perspectives. Chapter 6, Section 4 of the Airman's Information Manual gives a better description of NORDO procedures.

Another error is the top speed figure given for the F-15. That top speed is only accurate at high altitude with no external fuel tanks or weapons. Because the air is much denser at lower altitudes, the plane can't go as fast down low. When the F-15 first entered service, the Air Force conducted the Streak Eagle project to set as many world records as possible with their new plane. They went so far as to leave off the paint to make the plane lighter.

When you start hanging fuel tanks and missiles on a plane, the top speed drops pretty quickly, especially at low altitudes. Add to that the fact that the only way an F-15 can stay supersonic is to be in afterburner which drinks an incredible amount of fuel. Most fighters will have empty fuel tanks within 15-30 minutes when they stay in afterburner. Fuel consumption at low altitude is easly 2-3 times higher, too. There's the further concern about storming into some of the most crowded airspace on the planet at top speed, too. Then, you have to worry about shooting down a plane over a populated area, probably killing a lot of people on the ground in addition to everyone on the plane.

Hindsight is 20-20. It took the ATC controllers some time to realize something was wrong on that plane. Never before had a hijacked airliner been used as a weapon, so they had no way of knowing how bad things were going to be. Before 9-11, hijacked planes were usually directed to some other country where the hijackers made their ransom demands. Up until that time, airline crews were taught to cooperate with the hijackers to protect their passengers.

As a further complication, communications between ATC and NORAD weren't immediate at that time, so more time was lost there. You can easily poo-poo these facts all you want, but you'd just be showing how little you know of aviation and military operations.