If we are fighting Taliban , it does not mean rest of terrorists should be let off, the criminals should roam freely. Rather this is exactly the time to send a message to all terrorists that stop screwing around. Thats exactly what US did, IRA was declared a terrorist organisation by US after 9/11.
MQM is not equally toxic now, but it has all the potential to become one.
BTW you are acting just like Taliban apologist way of arguing, acknowledge all the crime committed by MQM or Balochs, yet coming out with a BUT factor, to trivialize, dodge, and oppose any action against them.