Given that many of the local tribes are no fans of the Taliban, and even the Taliban are not demanding separation from Pakistan, I don't think you have to worry too much a 'independent NWFP'. Thats is not what the insurgency is about.
On the other hand, Pakistan believes the Afghans and India are supporting various factions of the Taliban, the evidence regarding which was handed over to the US as posted above, so 'fighting that war' has a lot to do with fighting RAW as well - the two are interlinked.
While S-2 may show skepticism about the GoI's involvement, I completely agree with you on that point. This is not a view that is limited to you and other anonymous Indian posters on the web, but rather one articulated by a wide cross section of Indian intelligentsia (though I would not say a majority of it).
Retired military officials, bureaucrats, politicians - the list of contributors to this school of thought come from across the Indian spectrum. So I find it entirely credible that India is taking advantage of the situation in Afghanistan, and the US is turning a blind eye to that because of its strategic goals vis a vis China.
To think that the US is 'above' this kind of perfidy and duplicity is to forget the lessons of the past - of what the US did in Iran, of what it did in Latin America. To give the US a pass at this particular moment in time would be the height of foolishness, given the kind of Neo-con leadership in the Administration, and the views and opinions of the military leadership as well, which, IMO, by virtue of profession tends to generally align with the virulent Neo-Con ideology.
To add to what I have said earlier,
One must remember that India will not be the sole beneficiary from a weak and divided Pakistan although it might be the most obvious one, however, others, like Israel and even the United States will have something to gain.
Israel's position should be more or less obvious, Pakistan has a bad rep. of nuclear proliferation, to make matters worse it is an Islamic country and this is unsettling news for Israel. Mossad is arguably one of the best intelligence agencies on the planet. Israel, in my opinion, would rather have a 'strong India' (I'll get to it) given how the two countries enjoy strong bilateral relations and face similar threats. As such, I'm certain that MOSSAD would be more than willing to assist India with its objectives.
The omnipresent US, while the US presently needs Pakistan to assist it in its goals in Afghanistan, its services will no longer be required when the situation stabilizes (different story), something the US will work hard to achieve in the coming years. The way I see it, there are two ways for the US to reach a favorable outcome in south asia, one, somehow establish long lasting peace between India and Pakistan, leaving India free to counter China, or two, weaken Pakistan internally so that they no longer pose as much of a threat to India, leaving India free to counter China. The approach I believe (and I'm obviously only speculating, you may know better) they've taken is a hybrid of the above stated methods, they will work to establish and maintain peace, while gradually weakening Pakistan so India's threat perceptions diminish considerably. Moreover, the fact that China uses Pakistan to counter India will almost necessitate some kind of action on the US's part if it intends on balancing China with India. As such, I feel it is only obvious that the CIA is involved in destabilizing Pakistan.
Last and maybe the least obvious player (to me atleast) is the UK. I mean, you don't really hear too much about the UK innit? Britain faces a serious threat from homegrown terrorism, and maintains the largest intelligence network in Pakistan, if the CIA is helping, then lets face it MI6 is helping.
The insurgency may not be about an Independent country yet, but I remember reading this article somewhere about Pakistan fearing a revival of the 'Greater Pushtoonistan' movement, with RAW's new best friends, they might be able to pull it off, although this would probably start a war or something, not the best idea maybe.
It is really not as simple as fighting RAW anymore, Pakistan has bigger and badder enemies now. When I say India saw an opportunity and jumped into the mess, I really mean a mess.
You know, the only way out for Pakistan from the way I see it is the following. This will never happen, but oh what fun it would be if it did (and again, I'm speculating, I've only been at this for a little bit)
-establish peace (end all hostilities) with India immediately, do whatever it takes, both countries will have to make serious compromises, but it will have to be done. (kinda like the Uk and the US, kinda...)
-give china the finger and enter into a indo-pak-US alliance of sorts. You wont need china if you're cool with India.
-work together to stabilize Afghanistan.(I can think of many many benefits to this)
-work hard to eradicate Islamic terrorism from the region, by whatever means necessary (economic, military, diplomatic, you know the drill)
-20 years down the line we may have ourselves a truly prosperous 'block' that will probably be stronger than the EU and China, at least militarily.
-add Bangladesh into the picture so Munshi doesn't get offended.