Your reading of Afghan history seems rather short and selective to me. The rural areas there have been poor, fundamentalist and warlike for centuries, and so have consistently (and violently) defied all centralized authority. This fact was a central premise of British policy in the region, back in the day, and later directly led to the destabilization of the DRA (and so invited Soviet intervention) in the first place. The subsequent years have seen more fuel poured on the fire, but I don't see any basis in history for the idea that Afghanistan was a quiet, stable place that didn't pose problems for its neighbors, prior to the 1980's (or even prior to the 1900's).
Also, go and watch The VICE Guide to Travel, and you will quickly see how ridiculous the proposition that outside-supplied weapons are a determinant factor is. The Tribal Belt of Pakistan is the world capital of illicit small arms manufacture (not sales, but actual manufacture). It is a point of civic pride for them to have supplied the bulk of the small arms used by tribal fighters for the past century.
You seem to be trying way too hard to fit the reality of the situation into a reductive evil-foreigners-preying-on-harmless-locals narrative. The reality is vastly more complicated than that.
Also, it's curious that you refer to the "Muslim factions." I don't see what the particular religion of these people has to do with anything. Nor are they interchangeable with (or representative of) the vast numbers of other people who adhere to said religion. And they don't seem to refer to themselves in those terms in the first place. Other than a small number of AQ extremists, the militants there aren't fighting on behalf of "the Muslims," but for much more prosaic causes.
Likewise, there are "Muslim factions" among the ISAF: the Turkish deployment, for example.
