I certainly do not think there are Indian killing ‘terrorists’ in Pakistan who follow 'orders' from the state. Kashmir, however, is an internationally recognized disputed territory and not part of India (or Pakistan). Therefore, in light of our definitions, militias fighting Indian rule in Kashmir are not terrorists if they abstain from civilian targeting and other terrorist defining activities, which is what many separatist groups in Kashmir do (albeit not all, some have been infiltrated and directed by Indian intelligence, openly side with Indian forces and have human right records comparable to the worst of warlords in Afghanistan). I believe, as part of the recent reconciliation efforts between India and Pakistan, the Pakistani military did close down most separatist camps on our side, have arranged for the rehabilitation of ex-fighters (as was reported by the BBC at the time) and infiltration levels from our side have been overwhelmingly reduced (grudgingly admitted by the Indian Army). Furthermore, the Indian Kashmiri governor and other Occupied Kashmir officials have acknowledged that more than 95% of the insurgency is locally driven and based. Some infiltration or support is obviously inevitable, since Kashmiris on both sides do consider themselves one people and the terrain is perhaps the most uncheck-able in the world. Blaming Pakistan (or Pakistani Kashmiris) for all the violence is obviously an awfully convenient political pretext to ignore, and address, the serious issues represented in Kashmir.
So yes, many groups will undoubtedly reject the twisted Taliban strand of resistance in light of their own geo-strategic visions, which naturally in most cases do not include a local (and world) caliphate or replacing the Pakistani state. However, that having been said, the consequences of their abstaining are unlikely to be critical or significant, because like I said, they have other orientations.