I don't think that's accurate at all. The quote is more a recognition of the fact that the Federalists were against the idea of a westward expansion for fear that it would weaken the influence of the New England states and resignation of the fact that they might force through a split that would result in two countries.
But let us assume, for the sake of arguement, that you are correct and Jefferson is willing to let the people of the area decide. I still don't see any indication that once the decision was made Jefferson supported a later change. No pronouncements that any section that chose to join with and become a part of the United States could later unilaterally change their decision and go on their merry way. On the contrary, Jefferson makes it clear that he sees the inhabited parts of Louisiana and U.S. territory regardless. Earlier in the letter he speaks of Spanish Florida being incorporated into the U.S., no talk of choice there. And when he speaks of expanding states westward, he doesn't say anything about later independence for those same states. Sorry, but Jefferson seems to me to be someone who believed in the continuity of the United States, and not someone who thought that states should come and go as they pleased without any sort of restrictions on them at all.
And he seems to me as someone who wants our government to be something that remains becuase it is to our benefit to belong and support it, not because we fear the consequences of departure. Such is the nature of any "union" - which our country effectively ceased to be after the war.