Drones are a weapon with unprecedented leverage. They achieve, with minimal collateral damage, political and military goals that used to take firebombing of entire cities 60 years ago, such as the firebombing of Dresden in World War II.

A state's need to object to the actions of other political actors is generally in proportion to the ends being achieved by those actors. This is because ends are variably aligned, and bigger effects cause bigger absolute misalignments.

A state's ability to object, though depends on the means being used by the other party, because it is far easier to argue legitimacy and morality of actions based on means than ends.

For example, it is pretty easy to argue in most circumstances that torture is an absolute wrong, or that carpet bombing is a relative wrong in an age where smart bombing is available, independently of the ends being pursued. This is why, despite the overall moral authority enjoyed by the Allies in the calculus of ends being pursued in World War II, Dresden and Hiroshima are still effectively criticized by pacifists, and can be interpreted to allow Germany and Japan to reclaim some of the moral high ground in a historical assessment.

Drones throw this normal political calculus out of whack. The US is achieving its own ends at the expense of the long-term ability of Pakistan to achieve stable government-by-consent in its territory, by aggravating existing radicalization and making a hard-to-govern region impossible to govern. And it is achieving these ends with actions that barely rise above law-enforcement type operations.

So Pakistan has a strong need to object. However, the surgical nature of the means employed makes it difficult to do so. Pakistan's political job would be far easier if there were far more collateral damage through the use of napalm etc.

The problem with drones is not that they kill innocents on mere suspicion of being terrorists based on dubious identification, without due process.

That's dumb. That's a criminal justice/law enforcement standard of conduct being applied to military conduct.

The USAF is not a police department acting on behalf of a DA office. It is a military organization. And by military standards of conduct, drone operations are ridiculously sanitary and massively precise in limiting the amount of collateral damage they cause (to see why, consider the reverse case; how would you react if a police department blew up an entire building because they knew one murder suspect was hiding in there somewhere?)

So since drone operations are so clean, it is actually difficult to object to them as means, except through this silly reframing ploy of applying law enforcement standards to them (people thinking about the broader future of unconventional warfare will need to take this blurring of boundaries between military and police standards into account as they figure out new doctrines).

So Pakistan's only other choice is to object to ends.

This is a separate question, but suffice it to say that in the current geopolitical global situation, it is even harder for Pakistan to object to America actions based on ends being pursued (complicated situation involving the varied legitimacy of the Pakistani state in different regions of the country, the role of Arab money, gas pipelines, the moral case against Islamic extremism in the rest of the world, the China factor, the India-Pakistan equation...).

Which means that basically Pakistan is faced with an unsolvable problem in international politics. It is being ripped apart by forces larger than itself, and lacks the basis for objecting credibly to either the means being employed or the ends being pursued. And of course, it lacks the muscle to ignore international opinion and simply pursue its own interests more aggressively, the way China does.

Which is why it continues on its downward spiral as a failing state.

Which is sad, but not entirely unexpected. Though the south of the country can hope for a decent state, the north is part of the region historically known as the Graveyard of Empires. It has the misfortune of being something like the asteroid belt: ripped apart by powerful gravitational forces from all directions in such a way that states cannot really coalesce there. When the Silk Road was displaced by sea routes, there was hope for a while (and a fragile state did exist for a while). But then they struck oil in the Middle East and natural gas in Central Asia and the Soviets decided they needed an Indian Ocean port... and the region became a graveyard once more.

Basically, no known political operating system invented in human history can be installed in the region that is Afghanistan+NW Pakistan. We need to evolve beyond an international order defined by nation states for there to be any hope. Unfortunately that "beyond nation states" order is piggybacking on the Internet, which is going to take a while to penetrate deeply into that region.