I think the politicians have a bone of contention with just the Military leadership, not with the entire Army.
As you rightly said, these politicians have repeatedly accepted help from the Military leadership; in the same sentence you must also address the fact that the Military leadership has assisted politicians which they want to support and have made and broken alliances and Governments. Which part of the constitution gives mandate to the Military leadership to provide extra-judicial assistance to their favorite politicians?
The thing is, Military leadership is NOT immune to mistakes and when they become too rigid the tend to make mistakes more often then not. Their attempt to correct those mistakes too leads to other mistakes very often. And in the process they have to influence politicians, judiciary, bureaucracy, media etc.
In my opinion, the involvement of Military leadership in extra-judicial assistance to politicians and exertion of influence on other institutions and individuals need to be stopped. However, the Military leadership should be mandated to protect the interests of the country, overtly and within the jurisdiction of the constitution.
Bengalis claim that the Army was involved in murdering of highly educated innocent civilians, Professors, Doctors, Accountants etc. and raping of women. If that is an iota of truth to this, does it then mean that the Army allows raping, pillaging and executions? I am sure the Military too would have a mechanism to report abuse/misuse of authority to the higher command, for corrective measures.
Against whom?? Aliens?
You seem to have a lot of knowledge about Karachittes despite not having visited Karachi ever, and a strong opinion too which reeks of bias and ethnicity. And before you start labeling followers of Altaf Hussain as traitors, you need to label the Army as traitor for forming and supporting MQM; from inception of MQM to Musharraf!
And this is the dilemma of this country, label anyone a terrorist and a traitor when he/she is no longer useful or is demanding 'rights'.