Dear Bruce,

I think you misunderstood his meaning:

The patriots then and now were the people: Citizens, -whether in government or not. Of course the term "Patriots" assumes that whether you were in government or not, that you were right/correct in either serving the citizens, or in your challenge of a corrupt/tyrannical government.

The tyrants would be either tryants in the government, or citizens in society who were wrong (ignorant or self serving), in their challenge against the government.

Jefferson was clarifying his position that there will be people who challenge the government [and it's perceived tyranny], that will be wrong, (or ignorant of the facts of what is actually right and correct). That is inevitable.

As to those people, he was saying "[pardon them, or pacify them, (or kill them, if necessary, in defense of yourself and what is right)]"

...TJ again clarifies that as:

"[The Spirit of Resistance will often be exercised when wrong,
but better so, than not to be exercised at all.]"

...ie. No gun control

....and in that case, -you deal with it [the resistance] as is reasonably fair based on your own moral judgement to protect yourself, if you believe you are morally right, and the person challenging the government is wrong; that as a citizen (patriot) working for the govt. you still have the legal right to protect yourself.

Again.....

"[The Spirit of Resistance, will often be exercised when wrong,
but better so than not to be exercised at all.]"

...ie. NO GUN CONTROL

..., the reason for this is so government will always have a healthy fear and respect for/of the citizens, so it will not abuse it's powers or become corrupt, knowing that it (they) can be overthrown if they become so.

SO... TJ was saying that the civil liberties of all people should not be limited, for the sake of a few, (in government or not).

Everyone are citizens... but some citizens are civil servants.
Those in government serve the people.

He recognized that Innocent blood from time to time will be shed on both sides (government & civilian, right [patriot] or wrong).

Goerge Washington, John Adams, Thomas Payne, Alexander Hamilton, all reiterated (in various quotes) this emphatic belief
that you cannot limit or remove the rights of everyone for the sake of a few, (or you loose liberty as a society in it's entirety), and that the people must retain the right to challenge or overthrow a tyrannical government through any means necessary, including the use of arms.