Given the way terrorist cells work (with a high degree of independence) and the length of preparation needed for an attack, cutting off Bin Laden at 2000 would probably not be enough to stop the entire operation, as it is after the point where the "Go ahead" has been given. At this time, it is Khalid Sheikh Mohammed that is the main figure in the operation.
However, him being taken out of the picture could do all sorts of things. It's claimed by US authorities that he was being strongly advised by those around him to cancel the operation - so it could be that anyone replacing him might do so. It is also possible that it might be too late to call it off, or that his replacement still promotes it in his memory. It's important to remember how much Al Qaida would want "payback" for their leaders death. And with a major operation already in the final stages of preparation...
It's also alleged that Bin Laden pushed for the operation to be done sooner, and for it to be smaller in scale than what Mohammed wanted - with the latter wanting simultaneous attacks in Asia and six hijackings in the US. So, it could be that the attempt is scheduled for later and to be bigger, increasing the probability that intel services manage to find out about it and stop it. Equally, it could be that a later, bigger attack successfully takes place.
Each possibility opens up interesting timelines. No attacks would mean nobody would bother with the world's opium backyard, and it would trot along much like any other warlord-infested state. No attacks also make it hard to get the US public to agree to any kind of campaign against Iraq that goes beyond a repeat of 1991. But the Middle East is still a tinderbox of people who hate each other and who hate the U.S. Bush would probably want to go into some military endeavor, but he would probably have to be somewhat more limited in scope, which might actually make such an operation more successful.
If the attacks still happen, whether similar or more severe, the prior death of Bin Laden might have an interesting effect, given the portrayal of it being a "revenge" attack. I'm guessing that within the U.S, politicians would not be very keen to promote that line of thought, but is is always possible that narrow self-interest leads one side trying to blame the other and frame the assassination of Bin Laden as being "responsible" for the attacks. I'd judge it unlikely, but politics is dirty enough for stranger things to have happened. Abroad however, it could have a fairly important effect in convincing more people than OTL that the west "provoked" the attacks, which would strengthen the influence of Al Qaida. At the same time however, the lack of such a powerful and charismatic figure might well decrease their influence, so it's iffy.