I think it's about time I explained why Allen insisted that a little girl (Alex) fight in the Civil War.

At first, Allen respected Alfred's choice to keep Alex out of the fighting. But than, a huge misunderstanding happened. Alfred, just to make sure his baby sister stayed out of it no matter what, had the union invade New Orleans.

Quick fact: Alyx represents New Orleans being Union Seized. Where as Alex represented the people that had already been sent out.

So, Alfred unintentionally took Alyx away from Allen. So, Allen decided to fight fire with fire. He made Alex fight. It wasn't hard for him to find Alex is either, she was already traveling with him and the other confederates, just not fighting.

Wasn't Allen beating Alex/ordering others to beat Alex a little too far? Yes. But he was under orders from the generals.

It was just one big misunderstanding.