No, he was always a Union character, most notably Colonel Grierson.
You are wrong on this one. Wayne played Rooster Cogburn who was a rebel guerrilla fighter under Quantrill.
First Time I saw Duke as a Yankee was in How The West Was Won in 64/65 downtown Jackson Mississippi...
Even though he was playing Bill Sherman no one heckled in fact they sighed given he was sort of a cameo in that film...unexpected short role at Shiloh by Bloody Pond
It was Duke after all