A Lighter Shade Of Black

4 vs. Satan:
*The helpers (except their leader) may be callous and are supporting Satan, but they're not mass-murderers nor abusive of each other.
Alex in Princess Quest:
*NONE
The Stone of Power:
*RM: Artimus may be a mass-murderer, but he truly wants to stop the tragedy befalling his family, unlike the more self-centered Balthar. While we don't know much about him, the king of the east kingdom may be also pretty repugnant.
The Three Kingdoms
*Ishtal may participate in Palerius' actions, but unlike his boss and allies he doesn't resort to mass-murder. Made later more apparent when Palerius and Bertram kidnapped his loved one and made him participate, further showing him as the only remotely sympathetic of the bunch.
Dragondawn
*NONE
Harter Knall
*The S6-unit help their empire to get rid off revolution, but only because they're powerless against their king, who had people killed. Some even outright wish a better king.
Hero Story
*NONE
Kill the Demons
*NONE
Satan Saga
*Millie and Eron. Unlike their allies they're few antagonists to actually have some sort of a moral compass, while the rest of antagonists encounted in the game shows no hesitation about killing innocents at best and enjoys killing innocents at worst.
Story of Hero:
*NONE
The Legend of Devils
*NONE
The Sidestory Duology:
*NONE
The Time Of Bloody Fear:
*Eldon in route four. While he planned out the actions so he could become the king, unlike Maltros he doesn't destroys entire cities and cares about his people beyond in how useful they are to him.