Jefferson could often be a bit of a contradiction, I think depending on whether he was speaking of high philosophy, or was engaging in politics. I think Jefferson tended to be more pragmatic in his political endeavors. We all know this famous quote from the 1787 letter to William Stephens Smith. Jefferson, writing from Paris:
God forbid we should ever be 20 years without such a rebellion. The people cannot be all, & always, well informed. The part which is wrong will be discontented in proportion to the importance of the facts they misconceive. If they remain quiet under such misconceptions it is a lethargy, the forerunner of death to the public liberty. We have had 13. states independent 11. years. There has been one rebellion. That comes to one rebellion in a century & a half for each state. What country before ever existed a century & half without a rebellion? & what country can preserve it’s liberties if their rulers are not warned from time to time that their people preserve the spirit of resistance? Let them take arms. The remedy is to set them right as to facts, pardon & pacify them. What signify a few lives lost in a century or two? The tree of liberty must be refreshed from time to time with the blood of patriots & tyrants. It is it’s natural manure.
But that quote can be contrasted with Jefferson’s appeal to Edmund Pendleton, in 1799, regarding opposition to the Alien and Sedition Acts that were passed under the Administration of John Adams:
 Even the German counties of York and Lancaster, hitherto the most devoted, have come about, and by petitions with four thousand signers remonstrate against the alien and sedition laws, standing armies, and discretionary powers in the President. New York and Jersey are also getting into great agitation. In this State, we fear that the ill-designing may produce insurrection. Nothing could be so fatal. Anything like force would check the progress of the public opinion and rally them round the government. This is not the kind of opposition the American people will permit. But keep away all show of force, and they will bear down the evil propensities of the government, by the constitutional means of election and petition.
Jefferson may have had sympathy for appeals to the sword, but generally was committed to changing things electorally if the means were in place to affect the desired change.
There is also a twelve year difference between those quotes. I’m sure just about anyone can look back a decade or more and find beliefs which they no longer agree, or have otherwise changed drastically.
Don’t forget that Jefferson was also in line for the presidency by the time he seemed to moderate his tone.
There’s probably an element of contrarianism too, the British are trying to say that Shay’s rebellion is proof that America fails, and Jefferson is calling the bug a feature in response. Easy to say that a few lives don’t matter from a continent away. Unsurprisingly he was less keen on rebellion when he was in country and running for office.
The last line is almost always quoted in isolation with great enthusiasm by people who fantasize about being Wolverines. I’m not sure Jefferson was that much into it, even in 1787. He just doesn’t see how things can be otherwise.
When people fear the government — That is tyranny
When government fears the people — That is Liberty
Jefferson may have felt that peaceful means to change government was the preferred way to efect change, but the threat of violence as a last resort was needed to ensure that politicans would accept the change the people wanted.
Paul in Texas