I think there's room for siding with the magisters, but we need to understand their larger goals and motivations more to really say. It seems to me that Dallis is a source user, so her utmost goal isn't eliminating sourcerers, but to use them. If one could prove to be a willing minion to their goals, I could see some higher ups not caring that you're a sourceror.
Of course, it might be impossible to fit a magister playthrough within the context of the rest of the game if the prime motivation is running away from them. There's no point in doing a superficial magister-sided option, where it changes a few dialogs or quests here and there, but the game is fundamentally the same. If Larian hasn't decided from the get go that siding with the magisters is possible, than that's not happening now.