You certainly are spinning furiously. I notice that in your post you've put what you've read between the lines right there, in between the lines. Another equally -- if not more valid -- reading, is that Jefferson is just defending freedom of speech. Notice Jefferson does not say, "If there are any states that wish to secede, let them go." He does essentially say if there are those who advocate dissolving the union, let them stand undisturbed do not use force against them. Jefferson is speaking about tolerating errors of opinion. It is a plea for free speech in the spirit of Voltaire. He is not addressing what the government would do if a state actually tried to leave the union.
It would be interesting to find out how his contemporaries understood the speech. It would be strange if in this generally conciliatory speech Jefferson were essentially to say, "if you don't like it -- leave!" Even if there's a proviso that one can always return, it's not the of thing political leaders generally tell members of the defeated party. It's far more likely that he was assuring the nation as a whole that he would not violate the liberties, even of those who were most mistaken in their views.
Then again, using your method, one could argue that Jefferson was talking about those who want to get rid of the Montreal Expos.
"If there be any among us who wish to dissolve the Union or to change its republican form, let them stand undisturbed, as monuments of the safety with which error of opinion may be tolerated where reason is left free to combat it."
Freedom of speech was already guaranteed by the First Amendment. Somehow, I just don't think that when Jefferson states, "dissolve the Union" that he's referring to free speech. Why not just accept the literal meaning?