This is truly significant. Even if we suppose that his killikng is a one-off (maybe because he was not being cooperative and knew too much etc etc) and this is not a "genuine shift" in GHQ thinking (I think it IS a genuine shift, but just for the sake of argument), the end result is the same. True believer deobandi jihadists will leave the officially-approved Jihad world and move into opposition. Their numbers may be small and their ability to disrupt things less than it was advertised when their threat was magnified to get American money flowing or to explain why we couldnt "do more", but they are true believers. Without true believers, what will become of the official Jihad-machine and the two-nation theory? What asabiya will unite Pakistan? Sure, Gabon manages without deep Gabonese Asabiya, but we are not Gabon.
Interesting times.