Malistaire has a reason (!) to be evil. His wife died! Morganthe?!?! Noooo! She just wants to be stronger than Merle Ambrose, and that's it! No good reason. That is why I like Malistaire more.
When you get to the area before Ghost Avalon, the game will require you to transform into Gamma, and fight four battles (Young Morganthe is a pain), in which you will discover that Morganthe was meant to be the apprentice to Ambrose, but she crossed the line with him, when she obtained the knowledge of Zafarian magic (which was forbidden to her).
While her anger might be valid, Ambrose eventually learned to trust Gamma as his apprentice/pet. So, maybe her anger is focused more on Ambrose, BECAUSE of Gamma defeating her when she was young and had to cheat to win.