A very strong case can be made against the sort of business-as-usual manner with which this (mal)administration uses drones. Notwithstanding the fact that Pakistan's public complaints may be undercut by their private approval/consent to drone attacks, flying a drone into another country's airspace to attack a target is precisely the same as flying in an A-10 Warthog, and doing the latter would most definitely violate that country's sovereignity unless express permission had been given.
The problem with drones is that it is so much easier to slip a drone into another country, particularly the isolated, thinly-populated areas of a third-world country, without the sort of major repercussions that would result from sending in an A-10 Warthog that the temptation to use drones on a routine basis can become almost irresistable. This is particularly the case with liberals/leftists who have arrogated to themselves the high ground of the peacemaker and who are much more afraid of the blow-back from their own supporters and of the rank hypocrisy the use of an A-10 would expose.
Granted, cruise missiles raise the same sort of temptation; however, cruise missiles tend to require that you send the support infrastructure and the launch platform closer to the target country. Cruise missiles are also more prone to causing collateral damage since they are fire-and-forget and are not guided onto target by a live human operator. Both of those aspects raise the risks of blowback a liberal/leftist doesn't have the backbone to withstand. Drones do not raise either issue with as much intensity.
The underlying problem with this is that in many of the business-as-usual scenarios, the use of a drone is disproportionate to the benefits to be gained: the target to be hit and the risks of collateral damage - even though those risks are less than those occasioned by a cruise missile - and the business-as-usual use of drones can easily become immoral (and potentially illegal under the generally-accepted rules of war - not the UN b.s., but the ancient, time-tested rules).
Because of these risks it should be easy to see why a country like Pakistan would secretly approve of drone strikes while publicly decrying them: the risks of disproportionality and potential war-crimes accusations fall on the country that deploys the drones - the US - while giving the consenting country - Pakistan - to claim, at the least, that even though they authorized a degree of incursion into their territory, they never intended to, and did not, authorize such a disproportionate attack.
I'm sure others can make the case much more forcefully than I; however, hope that I have at least gotten the gist of such an argument.