The problem with your alternate is that since the USSR had invaded Afghanistan, and the US had funded and equipped the tribal resistance there into an organized larger-scale group, that the Taliban (and its support for radical Islamic organizations such as Al Qaeda) would still be there.
While probably there is less anti-US support for the radicals from the less-radical (if large-scale US forces are not present in Saudi Arabia), I fully expect there would still be some, and at least the operations in Sudan and Afghanistan would likely go ahead, as lower-scale terrorist activity would still conducted by AQ. Remember, 9-11 was not the first time that AQ had tried to collapse the WTC.
I do expect that the Iraq invasion would not go ahead, thus the US would have all of its attention on Afghanistan, which might well mean that is handled better and more-thoroughly.