He was writing at a time very early in the development of democracies, and democratic institutions. If you have a free society and democracy, then there is no place for violence.
Violence imposes an inequality in power in favour of those who are more violently inclined over those who are not. It further empowers the strong and further disenfranchises the weak or disadvantaged. Heinlein called voting the exercise of force, but that’s wrong, it is the ultimate exercise of speech. It’s having a say. The process of voting is one of giving all a voice. Violence is inherently anti freedom, anti speech, it is an attempt to silence or coerce others through intimidation or death. They are opposites. He called an armed society a polite society. Democratic societies shouldn’t have to be polite, they should be free to be impolite. Free speech means freedom to say things others don’t want to hear, otherwise it’s no freedom at all. Vetoing that with a threat of violence is tyranny.
So no, I’m sorry, I know Jefferson and the founding fathers of the war of independence are heroes in the US, but in the context of a democratic state he’s just flat out wrong.
If you have no voice, have no vote, or if the system is corrupt or unfair then sure. In that situation you don’t have a say, so violence might be justified. They were justified in taking up arms against Britain. But if you do have a say and resort to violence to impose your views anyway, that’s oppression.