The other day I ran across another statement by Thomas Jefferson supporting the right of secession.  It appears in a letter he wrote to Joseph Priestly:
"Whether we remain in one confederacy, or break into Atlantic and Mississippi confederacies, I believe not very important to the happiness of either part. Those of the western confederacy will be as much our children and descendants as those of the eastern, and I feel myself as much identified with that country, in future time, as with this." (Letter to Joseph Priestly, January 1804, in John Foley, editor, The Jefferson Cyclopedia: A Comprehensive Collection of the Views of Thomas Jefferson, New York: Funk & Wagnalls, 1900, p. 895)
In a letter to James Madison in 1799, Jefferson, citing "the true principles of our federal compact," suggested that Kentucky and Virginia should secede from the Union if the federal government continued to abuse its power; he argued that the citizens of the two states should "sever ourselves from that union we so much value, rather than give up the rights of self government which we have reserved, and in which alone we see liberty, safety and happiness" (in William Sterne Randle, Thomas Jefferson: A Life, New York: Henry Holt, 1993, pp. 534-536; see also Walter Brian Cisco, Taking A Stand, Shippensburg, Pennsylvania: White Mane Books, 2000, p. 18). (Jefferson used the pronoun "ourselves," of course, because we was a citizen of Virginia.)
Mike Griffith
Civil War website