No one is going to take away your right to self defense with fire arms. And once again you've abandoned law for political philosophy.
Jefferson also thought the Constitution should be rewritten every generation. Are we bound by that opinion as well?
The question was never whether Jefferson personally favored an armed populace. The question was whether his private correspondence carries the force of law. It does not.
More importantly, your argument proves far too much. If the purpose of the Second Amendment is to facilitate armed rebellion against the government, then you are conceding that the right exists for insurrectionary purposes, a proposition the courts have never embraced.
The Constitution created a republican system in which governments are changed through elections, legislation, impeachment, and amendment—not periodic armed uprisings. Whatever Jefferson may have mused about in a letter, the legal authority of the United States comes from the Constitution, not from selected quotations extracted from his personal correspondence.
In short, citing Jefferson's "tree of liberty" letter does not answer the legal question any more than citing Ben Franklin's jokes would answer a question about the Commerce Clause.