Issued while the Colonies were engaged in an armed conflict to impel that separation that Jefferson spoke of. That doesn't sound like the Colonists thought their actions were legal to me.
Now if you want to equate the Southern cause with that of the Founding Fathers, and agree that both resorted to rebellion to acheive their aims then that's a start in the right direction. But your position seems to be that the Southern acts of secession were legal, and it was Lincoln in the wrong to oppose them. That is like the Founding Fathers being surprised that King George got all ticked off over that Lexington and Concord kerfluffel.
Except King George didn't issue a Declaration of Independence asserting that you have a natural right to expatriate yourself. Indeed, King George's position was that expatriation is completely illegal and unnatural. It is the good ole US of A that proclaimed to the world that it is a natural right for people to separate themselves from unwanted governance.
We founded the country on collective expatriation, and then we rebuked the principle thereafter.