We've been watching the PBS documentary "God in America" and it was interesting to hear their description of how Lincoln's attitude toward religion changed as the civil war progressed. Initially it sounds like his thoughts were roughly the same as Dylan's With God on Our Side. As the war progressed though, and casualties increased, he felt compelled to the belief that this was all God's plan, that God wanted the civil war and wanted the north to win.
I suppose it was the only way he could think to justify all that pain. I wonder what sorts of beliefs about the afterlife Lincoln held that could foster anything but disdain for the Christian God. Initially Lincoln was more of a deist but his later belief, according to the film, was in a more personal (and rather horrifying) God.