Considering that Jefferson did not feel the New England states' beef concerning excise taxes during his Presidency qualifies as a reason to secede I doubt he would have thought either of these issues to rise to that level.
And on that you would be incorrect. Jefferson's letter to William Branch Giles, from which that quote came, was in reference to a resolution he was seeking to present to the Virginia legislature that would nullify John Quincy Adams' proposed tariff and navigation subsidy bills. He did so in language that was almost identical to the Kentucky Resolution of 1798 against the Alien and Sedition Acts, and went so far as to use the terms "null and void." Madison (who by that point of his life had come to support protectionism) convinced Jefferson to hold off until Congress passed the bills into law, but that didn't happen until after he died. The next year Governor Giles resurrected Jefferson's resolutions against the tariff and the Virginia legislature passed them, much to Madison's chagrin.