In the process of trying to establish the audiences' empathy with Jake Roedel (Tobey Maguire) the filmmakers slander the North and the Jayhawkers. Missouri never withdrew from the Union and the Union Army was not an invading force. The Southerners fought for State's Rights: the right to own slaves, elect crooked legislatures and judges, and employ a political spoils system. There's nothing noble in that. The Missourians could have easily traveled east and joined the Confederate Army.

It seems to me that the story has nothing to do with ambiguity. When Jake leaves the Bushwhackers, it's not because he saw error in his way, he certainly doesn't give himself over to the virtue of the cause of abolition.