Its hard to remove avoid MQM in Karachi especially in the present all time most unprofessional Musharraf regime. What I personally feel MQM and Musharraf have feeling for each other so its less political and more ethnic.

Solution is very simple and straight

Courts should be independent so promotion of judges on the base of seniority.

In army promotion of army men should be on the base of seniority so most senior guy should be Chief of Army staff.

This rule should be every where in all Govt institutions

Nawaz Shrif and BB should back and take part in election.
etc

Crystal clear election is the only solution who ever win should rule this country.