You do get a little bit more insight when the game is beaten.
(SPOILER)When all the characters are celebrating the Emperor's defeat, many of them vocalize their hopes and plans for the future. Leon however decides to leave because of his past deeds into seclusion, even though his sister begs him to stay. There is a reference that he might return someday when he is ready.
This makes me believe that he wasn't brainwashed and was acting on his own accord. He helped defeat the Emperor, but that alone couldn't wash away his sins.
A story of redemption told with only a handful lines of text.