India isn't going to seek a breakup of Afghanistan, something which is likelier to create instability on its borders than anything else. There's also reason to doubt that Pashtuns would be particularly separatist; OTL, NWFP was actually a stronghold of the Indian National Congress, through their alliance with the Red Shirts or Khudai Khidmatgar, and prominent leaders like Abdul Ghaffar Khan and has family were in favor of a united India. OTL, NWFP/KP province has actually been a stronghold of the Pakistani left.
Where I could foresee separatism is Balochistan, which was always very weakly integrated into India, much of it being ruled by various khanates. I'm not entirely sure that it would have been integrated into an independent united India at all: absent Partition, Indian leaders would have clearly prioritized retaining Sindh, all of Punjab, Kashmir, East Bengal, and the NWFP; I could see them cutting a deal with the Khan of Kalat for Baluchi independence, however.
Where I could foresee separatism is Balochistan, which was always very weakly integrated into India, much of it being ruled by various khanates. I'm not entirely sure that it would have been integrated into an independent united India at all: absent Partition, Indian leaders would have clearly prioritized retaining Sindh, all of Punjab, Kashmir, East Bengal, and the NWFP; I could see them cutting a deal with the Khan of Kalat for Baluchi independence, however.