I do not think that there is anything to worry about. For greater Pakhtunistan, Afghanistan would have to break up before Pakistan, as other communities in Afghanistan would not like Pakistani Pakhtuns to join them. Pakhtuns are around 40 percent of Afghanistan but with Pakistani Pakhtuns added, they would become around 65 percent of total population of Afghanistan.
Anyhow, I doubt if majority of Pakhtuns from Pakistan would like to be part of Pakhtunistan, as they would be forced to leave many areas of Pakistan, including many eastern areas of NWFP where majority are not Pakhtuns. Plus economically, they would become similar to Afghanistan, rather worse, because at present opportunities in Pakistan are open to them (even to many Afghans because of Pakistani Pakhtun connections), but after that, they would be foreigners in Pakistan, like Indians, with strong restriction in movement of goods, services, and labour between both countries. On the other hand, most Pakhtuns are patriotic Pakistanis who worked for Pakistan to their best, and thus many would not like to get separated from Pakistan, just to fulfil the ego of some who want to have 'Greater Pakhtunistan dream' get fulfilled. So, if such move would start in big way (other than for pressure purpose) than there is possibility that bloodshed would follow in big way amongst Pakistani Pakhtuns and those who would want separation. If this conflict would start between Pakhtuns than obviously Pakistan would then throw the separatists to Afghanistan and would close the border permanently between two countries.
As far as Balochistan is concerned, maybe a part of North Balochistan may become part of Pakhtunistan, that also, if Pakistani Pakhtuns of Balochistan would agree to it, and Baloch would get their part of Afghanistan. But there is no chance that rest of Balochistan would become part of Pakhtunistan, rather Pakistan may gain Baloch part of Afghanistan. Balochs have close tie with Sindh and both have similar historical background and large population of Sindh being Balochs. Zardari is also Baloch, though from Sindh.
So, this is all rhetoric but if majority really wants that and are serious, I believe they should have greater Pakhtunistan, and Pakistan should help them. Zardari has already started that help by promising to give a name. Maybe, it would satisfy their ego and if there would be any financial crunch for them later, they could fight with each other, strong tribe vanquishing and making weaker tribes slave, instead of causing law and order problem in Pakistan.