Jeff Culbreath, Catholic Imperialism: The Bulls of Donation
I don't think I'll even try to tackle this; the extent of papal authority must be determined first, and then whether it can legitimate conquest (the replacement of a native government by a government by outsiders).
Edit. Could it be that the pope is not acting as the highest secular authority, but merely as the superior of Christian princes, and acting in order to prevent a dispute between them (or something worse happening)?
(See also Mr. Culbreath's post on empire and secession.)