They are kind of the police on Elysium I guess. They don't really have anything to do with Deponia itself, they were only supposed to check whether there was life on Deponia before they let the planet explode.
However part of the Organon (Cletus, Argus) didn't really care about the inhabitants on Deponia, they just wanted to let the planet explode and get Elysium away from Deponia.
The Organon kind of developed a mind of its own because I don't think the council of the elders has ANY clue about what happens.
But yeah, you're right. What exactly their purpose is? I don't know. Elysium doesn't seem like the place where you'd need heavily armed clones. *shrug* I don't really care though, I really enjoyed the organon speech about asses.
