Sad to say, there is no real way to take out Al-Qaeda. For every member you kill, you've got annothe couple ready to avenge his death.
That's why Al-Qaeda is and was more of a threat than Iraq. You can defeat a country, you can't defeat a terrorist organisation that only needs a few people to carry out it's plan. That's why the IRA and ETA have been around for decades.
And now, the Iraq situation has just created more ill feeling in the Middle East towards the USA, and it might all come back to haunt Bush...