Main Hurdles:
The politician-judiciary alliance and the politician-bureaucracy alliance.
Very practical on paper, I dare say. However in the field this cannot work for two simple reasons:
The politician-judiciary alliance and the politician-bureaucracy alliance.
Both the institutions have been drastically politicized by the politicians and in time of need will naturally defend their benefactor. Perceptual bias against the army will encourage this tendency. The country, in the final analysis is run by the Patwari and Thanedar and they both fall under bureaucracy. The judiciary has a dismal record of performance for the last so many decades. A legal system that is so manipulable that it cannot quickly try and punish a currency smuggler, cannot be expected to do much. However the same system will be very swift in pursuing the army for its actions, particularly those proposed by yourself. A judicial system that can proceed against the army for Lal Masjid matter and some others in the same category, will not desist from pursuing the matter in a similar fashion, after the formation of national government.
Tragically, all the institutions of state are being run as personal fiefdoms except the armed forces where the service chiefs despite being very powerful in their respective domains do not grossly misuse their powers and remain within a certain boundary. There is no central nervous system to coordinate the functions of various organs. The clear manifestation of this is evident in current situation in the country from Jiwani to Khunjrab. The thugs rule the country and consider plunder their birthright, literally. The state machinery aids them in their pursuits, the lawyers aid them in the courts and on the streets, the police aid them in the police stations, the legal system aids them by delaying the run of the trial proceedings, the watchdogs aid them by hiding their follies and the international system aids them, first by accepting them as political refugees and then by looking away from their money laundering.
Equally tragically the army was so much negatively portrayed by the vested interest and foreign inimical elements that it was only a miracle that some of its esteem has been restored through Zarb e Azab.
Tragic it was that the sitting Prime Minister chose to side with a known anti-state propagandist in preference to an important state institution.
Tragic it was that the parliament stuck together to ward off effects of political agitation and never has stuck together for the people and the state institutions.
Tragic it is that a constitutional amendment empowering military courts to try and punish has been suspended from action by the judiciary upon agitation by a known anti-state activist. With such examples in our national life, it would take a lot more to give protection to the army for taking actions that you propose.
The first and foremost that has to be ensured is that the judicial system will not entertain any proceeding against the army for the steps that you have suggested. The only way that I see it happening is through providing a constitutional role to the armed forces (the army) for taking into hand matters that threaten national security while of course following a procedural path. These matters could be so diverse as external aggression, internal destabilization, sleeping with the enemy, financial terrorism, using threatening language against the state or its institutions, baseless propaganda against the state or the society, and so many others. Inaction on the part of the elected government to tackle the matters agitated would then pave the way for more direct action that would be unquestionable at any forum.
