I read something the other day at Border's that seems to have laid it out clearly. (It was in Crocker's PIG book dealing with the Civil War.) Were the colonies sovereign states, or were they colonies with a colonial charter, with ultimate sovereignty belonging to the Parliament? The question may seem to have a straightforward answer, but
Does positive law destroy any claim that there is a natural "right" to secession? Is a colony different in nature from an independent polity? On what grounds can the claims of the sovereign power by nullified? When can sovereignty or authority be lost? Is a colony bound to perpetual submission and obedience? What are the "legal" means for establishing independence? Is the only valid way through obtaining permission from the sovereign authority?
One could argue that the claim of sovereignty is invalidated when the sovereign power acts unjustly, or against the common good of the colony. What if it is an unreasonable extension of power? The principle of subsidiarity could come into play here -- decisions-making should be done in the colony as much as possible. (It would seem that some were content to accept this, with Parliament having ultimate sovereignty but exercising it only in certain matters.)
But do the virtuous have a right to rule that should not be denied?