Jefferson held that certain of these rights are inalienable. Those are the rights the people would not give up. The preservation of those rights, of which Jefferson claimed are Life, Liberty and the pursuit of Happiness is what motivates folks to construct a form of govm't. The protection of these rights are also what gives justification to the power exerted to form that govm't and for the govm't to claim just consent.
The authoritarian forms I mentioned deny inalienable rights. Right in those forms amounts to a claims made by certain despots that rule by the powers of force and deciet, not consent. The blessings of Liberty and Freedom itself are restricted to the rulers. The seat and the source of power in those forms is the govm't not the people. They may have a choice in who becomes a figure head, but they have no choice to modify the despotic nature of govm't imposed upon them.
Jefferson didn't agree that, "The only thing essential is, the will of the nation", to form a just govm't. The quote taken as is, simply reflects the truth of the fundamental fact that govm't is a rule of force. The quote doesn't address the issues of what is right, just, or proper. As is it's a description of mob rule.
A nation and a State are not the same thing, as Jefferson well understood.