President Karzai expressed some frustrations with the Westphalian model of sovereignty in dealing with the Taliban:
Afghan Pres. Karzai asks at news conf: Why is NATO unwilling to hit Taliban bases in Pakistan?"
In the AfPak region, Westphalian Sovereignty is, frankly, no more than an abstract concept. Tribalism, ethnic territorialism, and warlordism cut up the landscape. The line between Afghanistan and Pakistan is very arbitrary (see the ethnic map and map of "Pashtunistan").
Karzai wants NATO to take the fight to the Taliban, and believes the most effective military targets are in Pakistan (which makes sense--the Taliban keep more secure bases in the relatively safer region). Karzai is actively challenging the Westphalian model.
He's not the first to do it. Woodrow Wilson challenged the old European concept of territorial stability by suggesting that "a people" should have autonomy (though what defines "a people" is a vague concept, at best). The Israelis have constantly struggled in Lebanon where they have an enemy of extremist Hezbollah, but attacking Hezbollah in its own base means going to war with "Lebanon," where there are many neutral parties and even some allies.
Many Pashtuns want a "Pashtunistan," and many Baluchis want a "Baluchistan." Creating these areas would re-set the Westphalian territorial boundaries in the Afpak region to something more ethnically sensible, though obviously Pakistan and Afghanistan have little interest in giving up these large territories (unless they become so troublesome to hold onto that they are let go). The geopolitical need to hold onto them is relatively powerful, especially for Pakistan.
The Western dedication to the Westphalian Model may become a big contributor to the fall of the Afghan state, should it fall. But right now, the West has few alternatives. There is not another viable alternative to take Westphalia's place.