Maybe because, whether he was brainwashed or does things on his own will, Leon was so confused and frustrated after his hometown was invaded by the Emperor's imperial army. If I could make a realistic example, say there's one guy whose family was killed and their homes were destroyed by some army invasion. His reaction would include confusion and outrage, that would cause him to go against the army and then eventually aside with the enemy, because he was greatly outnumbered or was begging for mercy to live. After awhile, knowing more about the enemy well, he tries to control the army. But then, he was encountered by some of his surviving family members. He hesitated and then tainted with more confusion. He thought he lost his family and friends and feel that asiding with the enemy will only keep him alive.

Whether this scenario made sense or not to me, I think that's what Leon was going through like that guy. I really don't think he was brainwashed like Terra-Branford-brainwashed, but rather a confused being who tries to move on from the tragedy of the invasion.

Or perhaps SE purposely makes Leon a mysterious character that we had to think about what had ever happened to him after FFII. That's why we got fan fics.