I agree that Pakistan is not our friend, but that doesn't mean the time is right to make them an open enemy.
At this point its probably best to put what pressure we can on Musharraf, and continue to create a better environment for round two of this war. Northern Pakistan is worse than probably any other place on earth as an Islamic nutjob haven, but taking that region isn't exactly the best thing right now.
In the long run, I'd like to see these folks go back to being backwards, mountain hermits that won't marry a girl outside of the family. I think taking the Arab element out of the mix might just do that.
If not, and feet on the ground become absolutely required. I'd prefer they be Indian feet. If we pull all support from Pakistan and give India anti-missile capability and other support, Pakistan would be in a very, very bad way.
The Indian military is more than capable even today of crushing Pakistan, US support or not.
There is simply no comparison between the two.
India already has, btw a nascent anti-missile capability, with an S-400 network protecting New Delhi and certain other strategic areas.
IMO, the pakistani military is perpetuating trouble in Afghanistan with two purposes:
1) Theyre afraid of an increase in Indian influence in afghanistan.
2) Trouble in afghanistan keeps them in business with America, as a "frontline ally". More arms, more money, and legitimisation of military rule. The moment trouble in Afghanistan stops, people will start wondering about the jihad factories in Pak, and questions will be asked.