I agree, drones have their place and are a valuable asset, however there is nothing better (yet) then having boots on the ground. Whether NATO or Pakistan does it, this must be accomplished. Killing civilians have almost always pushed them into the arms of who isn't killing them. These civilians will never understand the terrorists disregard for their safety until the fighting gets down to a personal level.
Afghanistan is different from the Middle-East.
In contrast to terrorist groups in the Middle-East, the Taliban have almost no local support in Afghanistan. Their money and arms came from Arab sources and the Taliban's alliance with Al-Qaeda has been understood in Afghanistan as foreigners meddling in their country.
This is not to say that we don't have to be careful not to kill civilians just because they are unlikely to embrace the Taliban if we do. But the sensitivities are different. The clans of civilian victims want compensation for their losses, not us doubting their loyalty to whichenver non-Taliban warlord they happen to be allied with.
In Afghanistan, if you kill someone, you pay blood money. It's a system that has evolved as a solution to the same problem we in the west solve with life insurance.
The Afghanis understand that war costs innocent lives. Heck they have been fighting wars for decades. They know.
But they won't understand why we investigate why someone died rather than pay for it as we are supposed to. To most people on the ground it is obvious how someone died in an air attack.