It is believed that the 9/11 tragedy was largely carried out by Egyptian and Saudi nationals with the ideological and operational support of the top brass of Al-Qaeda, most notably Osama Bin Laden. Since Bin Laden and some of his cohorts were being hosted by the Taleban regime, it was a tricky issue for the US-how to extradite or possibly eliminate them. The Taleban refused US orders to extradite Bin Laden, saying they wanted evidence of his involvement in 9/11.
The question-What should the US have done, cannot be answered without highlighting the flawed nature of what it did, and trying to work out the alternatives from the underlying explanations of those failures.