I don't think Atomos is either good or bad, I think it just blindly feeds on aether and it distorts time and space as it grows more powerful, calling out creatures from the Void (just a mere side-effect). But that's besides the point.

The problem with Atomos is that its story is unresolved. We know that version 1's aetherites get all messed up, turn red-orange and stop functioning. We know that new aetherites are erected in camps and cities in A Realm Reborn, replacing the old, ravaged ones, but what's keeping Atomos from eating THESE? As far as we know, Atomos is still out there somewhere. There's no reason to believe that sometime between now and ARR, Atomos just goes away. We still don't know exactly how it appeared, why the Empire doesn't seem to mind it (or the voidsent creatures it summons), and we still don't know exactly how the aetherites were changed by Atomos's actions. That story arc is 100% unresolved at this point.

I doubt Atomos is just something that came, messed up things and then leaves for no apparent reason. It HAS to be more than a mere "WTF moment" in Final Fantasy XIV's story. At this point, however, that's all it really is.