"Evil" is a point of view. From our perspective, Zodiark may or may not be evil; we know next to nothing about Him and have had no personal contact with Him. All we have is secondhand information coming from Hydaelyn (as "The Word of the Mother") and his agents (the Ascians).

Either way, from what we've been told Zodiark's resurrection will mean the end of mortal life as it's known... and the people of Hydaelyn happen to like mortal life as they know it, so that's reason enough to oppose His resurrection.