This might just be conjecture, but I'm under the belief that if the Heavens' Ward and Thordan's "Primal Mode" transformations are really the same thing as a Primal summoning, it might just be that because they're sustained by the faith of Ishgardian citizens to "expunge any enemies that threaten the nation," anyone the Heavens' Ward perceives as a threat will still be attacked by their alter ego. It just looks like they're in control because the "Primal Mode" has the same basic goals, and we don't see anything of them outside combat.

Of course there's also the possibility they got Zodiark-Echo from the Ascians like the Sahagin chief, but we don't know that.