Humanitarian intervention and just war theory

Fr. Araujo recently posted an excerpt of Pope Benedict's address to the UN in which he affirmed a nation's duty to protect its citizens and the corresponding obligation of the international community to intervene when that duty is not fulfilled.  I'm wondering if others have thought about how just war theory applies to cases of humanitarian intervention when that intervention is likely to trigger an armed conflict.  The Bush administration's version of preemptive war does not easily fit within traditional just war theory, but does a preemptive humanitarian war qualify?  Specifically, would it be permissible for an international force to topple the military rulers of Myanmar if the international community concludes that effective aid cannot be delivered as long as they remain in power? 

Also, Pope Benedict cautioned that the international community's duty to intervene should not be understood as a limitation on a nation's sovereignty.   That confuses me -- how could it not be a limitation on a nation's sovereignty?  If we're establishing a principle stating that, if you engage in purposeful and systematic neglect of your citizens' basic needs, you forfeit the right to exclude foreign governments from your country, and perhaps your right to govern, isn't that a limitation on sovereignty (and a prudent one at that)?