"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?
I don't see support for secession in his words, just an affirmation that he would uphold the principle of free speech which Adams had violated. After all, he's willing to let not just secessionists but also those who would change the "republican form" of the union stand undisturbed. It would be very hard for them to change the republican form of the union when Jefferson had the Presidency and his party controlled Congress, and if they seriously tried to impose a non-republican regime, Jefferson would surely oppose that. Therefore I presume he's talking about speech, not about an actual act of imposing a non-republican government, which Jefferson would be bound by his principles and the Constitution to oppose. If he speaks of letting those who want secession and what he'd call tyranny or monarchy alone, and if we know he would fight rather than see actual monarchy or tyranny imposed, then it doesn't look like he's making the most rousing endorsement of secession. I don't know what he would have thought of secession at the time, but I do think the sentence is somewhat different in meaning than your interpretation.
Jefferson is an interesting case. He was much more radical than most of the rest of the Founders. And here he is in 1801, an old revolutionary and oppositionist, trying to keep his opponents from rebelling or revolting against his own authority. In time, at the head of a government, with obligations and responsibilities, Jefferson moderated his earlier views in practice, though not always in theory.