The Baloch separatists are relatively small in number and lack sanctuaries (NATO will probably push them out of Afghanistan one day in exchange for safe exit from Afghanistan) so they may be a nuisance for the Pak army but they are not a critical problem (that, at least, is the Pak army view).
Killings of Shias are unfortunate but cannot be helped because the main anti-shia militant group (LEJ) is connected with the same networks that are our "strategic assets" and cannot be cleaned out without jeopardising the "good jihadis". They are also funded by our brothers in Saudi Arabia, who are going to be ever more essential once the US dollar stream finally begins to dry up. It is sad, but sometimes that is the price we pay for mining copper at Saindak.
In short, killings in Balochistan will be a human rights issue, but will not have any "strategic" impact. On all sides, the "deep strategic thinkers" understand that some eggs have to be broken in order to make an omelette. In Pakistan, we will break many of them and not even cook the omelette. Sometimes, things don't work out so smoothly. What can one say..