You did not understand my point... In principle what you are advocating is correct, but it is not always so in reality. Here I will relate to you a story from the Prophet and his Sahabas.
Two opportunists, Uynaynah and Al-Aqra Ibn Habis, came to Umar (RA) in medina while he was sitting, and they wanted a piece of land in Medina, they had first went to Abu Bakr (RA), Abu Bakr's advisor told him to give him the land and Abu Bakr agreed with his advisors, but Abu Bakr decided to give the final consent should these two men get consent from Umar (RA), Abu Bakr advised that he will allot them the land should Umar (RA) agree to it first and he wrote them a piece of document, when Umar asked for that document he tore to shreds, the opportunists enraged exclaimed "What have you done Ibn Al Khattab, this is the Caliphs document" Umar responded, "Has he not said it is valid unless I accept it, by Allah I do not accept, go Back... What have you done for Islam to be awarded with a large piece of land to be your private property" and they responded "Don't you know that God's messenger gave us some spoils of war" Umar then responded "God's messenger wanted to win your hearts over when Islam was still weak. Now Islam is strong by God's grace. Go away and do your best.
You see how when Rasullulah was alive he had to make so many concessions to so many opportunists because Islam was weak, and he had satisfy these type of criminals so that he could make Islam stronger and follow the principled path afterwards.
The same is true for Pakistan, Pakistan unfortunately is weak right now, you have criminals everywhere, and Pakistanis are divided, and the main reason behind this division is because you are not following the system of Islam. If everyone followed Islam or at least the majority did by tooth and nail, not just on a social level but also on a political and judicial level, then there wouldn't be so many disagreements, you wouldn't have to argue amongst yourselves over executing a criminal or not as that decision would be clear as day and night, but because that decision is not clear as day and night you must out of necessity make concessions such as this, you must overlook the criminal tendencies of some criminals, until your nation truly follows Islam.
This is why I said in the beginning "If hanging Musharraf is going to divide Pakistan and weaken Islam and Muslims then it would be best to avoid it, but if it is going to make Pakistan stronger and strengthen Islam and Muslims, then go for it."
But until Pakistan becomes a strong nation under a Caliph and I mean so strong and orderly to the point that if a donkey dies because of some mismanagement by an official, then that very official will be held responsible by the Caliph for having allowed the donkey to die because of some negligence, until then you have to for now put up with this.