Finding Mullah Omar and cleaning out all of the mullahs would be a good start.
The international community does not see them as criminals. Majority of mullahs, maybe even including Omar, did not know about 9/11 in the making. A genocide is always an option, of course (and that's what it will take to rid Afghanistan of mullahs) but I don't think this will be looked at kindly by practically anyone, anywhere. A good number of today's Taliban mullahs were just teenagers in 2001, and they were fighting foreign troops for most of their adult life. Wouldn't we do the same if the USA is occupied, for example, by Chinese troops?
Mullah Omar's guilt is only in the fact that he was a bad administrator. When W wanted OBL extradited Omar started the traditional oriental negotiation dance that is usually scheduled to last a few months. W had no time for that foolishness; Omar's regime was kicked out, and AQ was rounded up, and their training camps are no more.
But after that was done I have no idea what one could do in Afghanistan, short of growing opium or building rock gardens on a scale of Nazca plateau. It's not exactly a friendly land even if you are a local. Are US troops working for the mayor of Kabul, a.k.a. the President of Afghanistan? By all indications they are; Karzai cannot hold even the capital city with his own trusted men. As soon as the US army is out of Afghanistan Karzai will hang from the nearest streetlight. His recent gestures toward reconciliation with Taliban are pointless; Taliban, being true children of their culture, will shake hands with their enemy and immediately order him killed.
In other words, the USA constructed an inverted, unstable pyramid of power in Afghanistan and is simply afraid to upset it. That's why Karzai remains in power, supported by US troops - and that's why the troops cannot leave. Nobody is willing to be responsible for the big crash.