As another user mentioned, Zeus just imprisoned the titan because he wasn't powerful enough to kill them (Chronos, by contrast, DID kill his own father). Also, it's well established as part of the scenario that the Archon (when awakened) is more powerful than any of the gods (he seems to make them very nervous).
Zeus CAN definitely interfere with the Archons plans, and cause a great deal of annoyance. However, in a direct confrontation, Zeus would lose pretty badly. (Did you read the dev's post a few pages back about the origin of the gods (in this game) and the role of the Abyss in the story? Much of my assertion is based on that explanation.)
Of course, this is all just speculation (sort of like debating who'd win in a fight between Kong Kong and Godzilla). We'll see how it plays out as the story progresses.
You know a game is good when fans are debating like this about the story possibilities. I half-suspect Kyois watches these debates and is basically letting us write the story for him.