Save for the yeoman effort of the "Let Us Build Pakistan" collective newsblog, which is run more as a supporter effort than a professional communications effort, no official media group has tried to parse the killings that have been going on in Karachi since the beginning of May.
Until Dawn bought it up here.
My personal opinion was that the MQM was killing off Pashtuns to scare the new wave of migrants driven by the war in the North from settling in Karachi. They were probably sure that they can't scare off Pathans who have been living in Karachi for decades (cause if any long time resident was going to flee, with all the violence, it would have happened by now), but to prevent a new wave of Pathan migrants into Karachi. And relating to the targetted murder of Shia professionals in Karachi, LUBP has a rumor of Pakistan establishment spawned religious militants, showing their sectarian stripes and not being reeled in by the Establishment.
Aside from the sectarian angle I'm quoting, the Dawn article fingers the three way smoldering struggle between the MQM, ANP and PPP in a fit over demographic changes. How the sectarian killings could fit into it would involve Interior Minister (and all around incompetent) Rehman Malik's "third force". If he means India or the US it's just more Rehman Malik BS. Nobody thinks JSOC shooters are hunting down Shia doctors in Karachi, nor is Indian intelligence involved with this new generation of MQM shooters (who I vouch, do exist, but are not visibly active) the way Indian intelligence was involved with MQM militants in the early to mid nineties.
If you do want to account for a "third force" to account for the dead Shia Doctors (Observe LUBP's true but provocatively titled post Kill a Shia Doctor a Day) the only force you can think off is Al Qaeda. But let's again get serious, there are hardly any Arabs sitting in Karachi planning murders of Pakistani Shia Doctors. For the money those type of fuckers could command, they could probably afford to hire ten Pakistani Doctors, have them called to the Gulf and then off them as they please. No, we have to look at somebody who is not local to Karachi, but close to Al Qaeda to follow their sectarian chaos theory of killing as many people as possible for maximum political impact. Lashkar-e-Jhangvi anyone? And yeah the video that LUBP post starts with is from January 2007, when this problem was more or less dormant.