This is a real threat to future of Pak and since jihadis will eventually have access to Pak nukes India cannot but help USA and Pak to actively target these jihadis. Musharraf is vulnerable and nothing will go right for him now.
In fact the jihadi moves are comparable with the 11 th century battles of Turks and Moghuls (Genghis khans and Mohd. Gaznavi)against locals to establish cruel Islamic empires than with any human rights based struggles.