Much of the evil that is done in this world is done by people who believe that there actions are right, even that they themselves are acting against some evil. Take, for example, the Unabomber, Theodore Kaczynski. He didn't get a walk because he believed that what he was doing was right. But you seem to be suggesting that I should excuse Lincoln on such grounds.
I would however quibble with your hypothesis that Lincoln himself believed that Southern secession was wrong. We can never know what was in his mind, but his actions can equally well be explained by the assumption that he saw secession as a monkey-wrench thrown in the works of his implementation of the "American system". It would similarly completely explain his opposition to the extension of slavery to the territoties.
One's viewpoint towards others does tend to be slanted by ones beliefs. I no doubt view the intentions of the southern leadership with the same kind of suspicion that you view Lincoln's. So be it. We won't convince the other, but I suspect that neither one of us will stop trying.