Well unfortunately, the Pakistani Army/ISI doesn't think like you do and that is the tragedy of Afghanistan.
Even Musharraf has clearly said now that Pakistan will support the Taliban and Haqqani network in Afghanistan. So is it any wonder that Afghans hate Pakistani Army/ISI?
Musharraf has never said Pakistan supported the Taliban, or the Haqqani network. No high level official in Pakistan has ever said that. Pakistani officials have always said they want a regime that isn't hostile towards Pakistan. That is all that is required from Afghanistan, but they fail to fulfill even that.