While we don't know if Zodiark himself is evil... everyone who claims to work for him really doesn't like the world as it currently is working and is actively working to change that. And from the looks of things, they don't care about what happens to all of the life that is currently living in the world.

The people who work for Hydaelyn meanwhile care a lot about the world and what happens to the people in it. They want them to have as much agency as possible and to not be bothered by the Ascians who are trying to wreck things.

So while that doesn't necessarily say that much about Zodiark or Hydaelyn, it does say a lot about the people who ally themselves with those entities. And one group of those people are a lot more evil then the other group is.

Until we get to talk to Zodiark himself, that's good enough for me. It's Zodiark's followers we interact with on a regular basis and not Zodiark himself as it is.