Bee-dubya-ell, that's an excellent and well thought-out suggestion as to the story behind the song. It seems to me to fit the words and the atmosphere perfectly. Thank you for that! :)
Obviously, we can't ever know, and Bobbie Gentry didn't even know either. But it's always intrigued me, and every year the same thoughts come to mind on the Third of June.
Not knowing much about the location, social structures and history of the area, I couldn't have formed such a likely explanation.