As much as I despise Saleem Safi for the soft corner he sometimes shows for JUI-F , this show and his overall understanding of the situation with respect to Pak-Afghan relations deserves special attention.
He is right on the following points:
1) Pakistan should accept the fact that Afghanistan will continue to lean towards India for many years to come.
2) Ultimately, "trade" will be the only long term strategic tool that Pakistan will have over Afghanistan.
3) Closing borders or making trade a hardship will only isolate Afghans, and their dependency will slowly decrease if they start looking for alternate routes.
4) The sooner Pakistan makes Afghanistan dependent on energy needs and on royalties from pipelines, the better it is.
5) Allowing cross border cultural exchanges and easy travel for education and health will ensure that a steady relationship and dependency exists.
If Pakistan tries to isolate Afghanistan and use its superior military for raids in its territory, it could turn out to be an absolute disaster. You lift a brick in Afghanistan and you will find haters of Pakistan swarming underneath it. These haters can only be won over by making them realize that Pakistan and Afghanistan have historic ties and there is a significant trade/energy dependency.
As Safi points out, even the Afghan-Taliban are sceptical of Pakistan, therefore making enemies of both the Afghan government and Afghan Taliban at the same time by doing military raids in Afghan territory is a dangerous ploy - one that India will be very happy about.
Lastly, one of the biggest hurdles in the merger of FATA with KPK is the definition of the Durand line. The merger will not be possible when hostilities between Pakistan and Afghanistan are high.