Their first target was not PPP or Sindhis, they even sympathized with a lot of Sindhi nationalists and tried to gather them together against what they perceived to be "Punjabi" Military/industrial influence. APMSO was helped by PPP's youth wing in the start, and their main fight was against Jamiat not ppp's student wing. MQM wiped out the vote bank of the religious parties, mostly Jamaat e Islami. They never really made any inroads in to Sindhi territory.
Sure, I am not privy to all the happening of PA leadership so you may indeed be right, but I had relatives who were part of the military operations in Karachi in the 90s. I am just telling stuff I've heard from people closer to ground zero.
Yar, Musharraf ko to uske dor mai t.v pe saray galliyan de rahay thay.
But I agree with you that there should be more accountability, and if military rulers, starting from Ayub Khan, had been held accountable, we wouldn't have had the curse of later military rulers and their political pets like Nawaz, Bhutto etc being imposed on us.