Per the Constitution, rights are something accorded an individual that comes from God. Powers are something that individuals delegate to governments to perform on their behalf. Secession would not be a right, but a power so how exactly would Jefferson here be talking about secession?
I guess we all have a right to secede at any time by simply moving to another country.
Not all "rights " come from God. "Rights" can be established under a contract or compact. If I enter into a contract with a builder to build a house and he doesn't build it to my specifications per the contract then I (usually) have a right to void the contract. It was of such "Rights " that Jefferson wrote. Instead of calling it secession he called it rupture.