There is actually a track record for this sort of thing working out - several 'edgy' writers who otherwise loathe superheroes with a passion have admitted to at least having an appreciation for what Superman stands for, and have written him accordingly. If Millar follows through on this attitude regarding a character who's basically a Superman/Captain Marvel archetype, we may actually be able to get to the end of the story without anything horrible happening.
Interesting that the evil space monkey is playing both sides against the middle. It's not often the same guy who gives both the hero and the villain their powers - although I suppose this could be a commentary on the wizard Shazam and Black Adam.