Musharraf ruled the nuclear-armed state after his 1999 coup through tensions with India, an atomic proliferation scandal and an Islamic extremist insurgency.
The case was related to the state of emergency he imposed in 2007 while in power, officials said.
Police in southern India have arrested three people in connection with the deaths.
Pakistan's powerful army chief, General Raheel Sharif, has stunned his supporters and critics with Monday's unanticipated announcement that he would not seek an extension for his job when the duration of his service expires in November.
December marks two anniversaries in Pakistan's history, one through which more than half of Pakistan's population seceded to form a separate country, and the other marking the most heinous attack on schoolchildren ever in that country.
In Balochistan, only one man, the chief minister, has benefited from the conflict between Islamabad and the Baloch separatists. He has betrayed both the sides without even making them notice. Who wouldn't blame the Indians if the price is so awesome?
Many Pakistanis are torn between their support for democracy and civilian control of the military, on the one hand, and their desire for social and political reform, on the other. Just as Sharif is the flawed advocate of democracy, Khan and Qadri's calls for reform have been tainted by their covert ties with the military and its intelligence arms.
We Pakistanis are long past faith in our institutions -- often, we're the first to suspect that they've played a hand in ruining our nation. We just don't like it when the West points that out. All this fear and cynicism make for a heavy burden.