Tribal militias allied with the government helped block a Taliban advance in this corner of northwest Pakistan close to the Afghan border, but their success has come at a price: the empowerment of untrained, unaccountable private armies that could yet emerge as a threat of their own.
Fine. Point taken. The Taliban are a threat right now. The militias are being used to defeat the Taliban threat. One day, the militias could become a threat.
But that kind of problem is true in any conflict where you arm the people to resist an enemy. And that includes enlisting lots of your people into an army that suddenly loses a former enemy to occupy the attention of those soldiers. That was one of the problems Saddam had after the First Gulf War (Iran-Iraq War). He couldn't afford to keep his army on the payroll yet couldn't afford to demobilize it both because Iran could surge across the border if it wanted to restart the war they lost, and because putting lots of (partially) trained (especially Shia) soldiers back on the block wasn't necessarily the smartest thing to do.
So, yeah, this is a potential problem. But it is no reason to fail to mobilize this resource to defeat the current threat of the Taliban since the government's other resources aren't sufficient to battle the Taliban.
And really, what problem would you rather face--internationalist Taliban who love suicide bombings and bring down foreign interest in your land with no regard for the damage the area they are in endures? Or local tribal forces tied to their location that they want to defend? The Pakistanis, in one form or another, have been dealing with those mountain tribes for a long time, and can manage that local problem far easier than fighting hopped up jihadis intent on.
I don't ask that every solution solve every foreseeable problem ten steps down the line along with the problem to be solved. I just want solutions that solve the immediate serious problem without obviously crippling me for the next step.