Tom Clancy predicted terrorists would fly planes into buildings in 1994's Debt of Honor, which ended when a plane was flown into the Capitol building, killing the President and most of Congress
It seems that between 1994 and 2001, if somebody took this work of fiction seriously, they might have thought to either secure cockpit doors and/or change the operating procedure in the case of a hijacking. Obvously, the first change was suggested in a governmental report, but it was killed by Gore in exchange for campaign contributions from the airline industry.
My question is, was there ever any discussion of changing the was airlines respond to hijackings prior to 9-11?
I don't know if there was any discussion. But speaking of Tom Clancy's prediction, I also remember that the pilot episode of the X-Files spinoff The Lone Gunmen, which aired March 4, 2001, involved a plane crashing into the World Trade Center:
The Lone Gunmen: 1AEB79 Pilot (4th March 2001)
They realize that the airplane will be remote controlled, just like Bert's car was. Talking by phone to the Gunmen's office, Byers asks Langly and Frohike to hack into the aircraft controls. They do and discover that the plane is programmed to crash into the World Trade Center.
So both Clancy and X-Files writer Chris Carter had thought of the idea; and usually those guys base their plots on researching the topics they're writing about by consulting experts, so it tends to follow that counterterrorism experts had also at least entertained that as a possible terrorist scenario. Whether they considered it as likely as other possible scenarios is another issue.