EMP does exist. However, if a 767 was EMP'd, the effect would be to degrade or destroy the avionics on the aircraft to the point that any effort at remotely flying the aircraft would fail.
The article has numerous technical inaccuracies; this is only one of them.
AWACS aircraft are used as sensor platforms for managing airspace in wartime. The do not have the ability to remotely control aircraft. The most "controlling" aspect of their operations is that intercept controllers on the AWACS talk to interceptor pilots on the radio and tell them where the bad guys are and which way to steer to intercept them.
September 11th was a particularly nice day on the east coast (I was in Washington for a business meeting), so "IFR" (known in the aviation community as "I Follow Roads") would not be necessary. However, the hijackers could crank in GPS coordinates into the navigation system, engage the altitude hold mode on the automatic pilot, and then go to manual control and aim visually as they approached the Trade Center.
This theory gets put up from time to time on FR, and anyone who knows anything about aviation in general and military aviation in particular shoots it down right away.