I have no inside information. My closest encounter to the Indian Intelligence establishment was meeting R. N. Kao at his brother's house in Washington DC in the late 1960s.However I am not sure if its agency are engaged in this civil war. There may well be camps somewhere for "mukti bahini".
Yet, we have seen repeated attacks on ISI facilities since Mumbai. The most recent attack may have been on ISI or ISI attached to guarding Pakistani nuclear facilities. And this isn't simply Israeli style 'eye for an eye' retaliation that makes us feel good and that the Mahatama warned against. No, these attacks are targeting the controllers of the terrorist organizations.
Do Indians have so little self-esteem, that we can only view these attacks as some kind of Taliban/ISI internecine warfare?
The Indian Army was so close to avenging Kandahar by installing the Northern Alliance in Kabul.
Surely, it can be argued that if not for 9/11 and the incomptent reaction of the USA, a pro-Indian government would be Kabul and Mullah Omar and Osama bin Laden would be with their 72 virgins?