You are right, this is what brings discontent among the populace of Pakistan. But there is an inherent problem in such admission. Because the drones come from the US, the people would reject their utility not matter how tactically and strategically useful they are, and the resulting consensus could bring the intel agencies in the dock. Also, a great number of people actually do support those who are specifically targeted by the drones. Calling Hakimullah Mehsud a martyr by a political cum religious leader was just a peek into that attitude.
How can you expect the intel agencies to speak on the usage of drones when political parties such as the PTI and the JeI are amassing crowds to oppose the same?
No. In India, irrespective of the merits of such intervention, anything, which is foreign and unpopular in public, would bring down the government fairly quickly. Bhopal gas tragedy is just an example where the owner of Union Carbide was not at as big a culprit as he was made to be and the company was sent packing the very next day and compensations were sought right away.
They had no choice. While the usage of has in fact kept Pakistan calmer than it would be, the Army would lose its credibility among the masses if it were to make its support for drones public. The Salala incident, Kamran Air Base attack, and then the OBL raid, all these incidents have already made the Army look weak in the eyes of masses. How can they afford to tell the people that what everyone is talking against in the country, the Army is actually supporting it?
It would not be easy for anyone to make the commoner understand the benefits of the drone attacks. Most certainly not for the Army.