You admit that "war on terrorism" hasn't been America's priority and that it's possible for a civilized country to have its interests furthered by looking the other way or supporting "freedom fighters". It would be highly unreasonable to expect American enemies to be very sympathetic about the events of 9/11, especially if those were bombed by America, and make it a pre-text for a war.
The official position of a government matters little, because the terrorists are often supported by rich individuals or through semi-official channels. The Saudis have done much more for the cause of jihad than a (relatively?) secular Saddam. Saddam could have been an American friend just like many other dictators in history.
The same, of course, with that place, Washington: it can change policy under pressure from Washington and begin cooperating with Washington. To a degree.