I think some of the recent justification for attacking the nation-state-as-proxy is built on the proposition that if a government fails to fight against the combatant groups within their geographical boundaries, then the nation-state becomes culpable. Witness, for example, the better-looking relations between Israel and the Fatah-run Palestinian government, which was actually using its police power, at least sometimes, against those launching attacks on Israel.

In the current Palestinian situation, I'm not even sure your analysis applies, since of course Hamas is the democratically-elected governing party, as well as being the military organization. Saying that they don't have full support of the people is a bit like saying that only Republicans are at war in Iraq. Things are not so clear with Lebanon, where the concept of "political party" is different from anyplace else I know, but Hizbullah is one of the five or so largest blocs in the parliament, and one of the two representing the Lebanese Shia population.

(By the way, this seems to me entirely different from Iraq, where there was no connection to either al Qaeda or the Taliban.)