That’s not Executive Orders.
I believe you’re thinking of Debt of Honor:
http://en.wikipedia.org/wiki/Debt_of_Honor
I thought Clancy used the scenario twice, to end one book and to start the next. Captain Sato is assigned to fly a damaged, empty 747 from Washington to London. He knifes his copilot shortly before takeoff. Then he dives into the Capitol in the middle of a State of the Union address.