if people listened to the 27th december episode of aapas ki baat, they will recall najam sethi mentioned that he got a "phatkar" (scolding) from a pakistani general on his criticism on the role being played by the pakistani security agencies/establishment (PA/ISI/IB/etc) in balochistan.
i think these threats are a culmination of a few things. najam's criticism on establishment's role in balochistan, establishment's role in handling of foreign policy, internal security, how they have made the present democratic government a puppet and the pak establishment does definitely see najam sethi as a CIA operative who tries to form and influence the opinion making of people in pakistan.
those who regularly follow aapas ki baat, will notice, najam sethi from initially being pretty critical of the role of pakistan establishment had significantly toned down for quite sometime now, this video should explain why that happened.