While I agree that prayer scene may have been a stretch, it may also have been a way to bring the thoughts of Jim and Jackson out into the open. I thought it was a wonder they even included the Bonnie Blue Flag, not many would go against the grain of correctness to do this. There are of course a lot of things that could have been done another way, but the important points were made, unlike some other 'period' pieces.
I was very moved by the intro and credits with the flag representation. It was beautiful.