End-game is different, and the selection criteria of the people being murdered is different.
End-game:
Empire zealot is working toward a world in which the Empire reigns supreme and oppresses all of Thera. It's also explicitly evil to the extent CF associates "darkness" with "evil" and "light" with "good". Consider the slogan "<b>Darkness</b> and Order".
Maran is working toward a world in which everyone who is inherently evil has been eliminated. So, no more psychopaths mass-murdering people. No greedy bastards robbing people blind. No death mages killing people just to experiment on their corpse. Etc.
Target selection:
Empire zealot kills anyone who won't join the Empire. It's coercive with the goal of forcing everyone to get on board.
Maran kills anyone who is evil, specifically because they're evil. They're not trying to force anyone to join Fortress. The only thing they're trying to coerce is for people to not be evil. Which, presumably, is for the benefit of the innocents who suffer because of the evil person's actions.
But yes, to the extent both groups are "zealous", they're similar.