This question contains spoilers…
(view spoiler)[How could the universe have been balanced when the war ended if the Sephiroth was locked up while the Malachai was free to wreck havoc? (hide spoiler)]
Both the Malachai and Sephiroth are bound and enslaved. The Malachai was in hiding from his master so he has never been truly free. He had to be very careful, otherwise he'd have been found and dragged back to Noir. It's why he didn't assemble his riders and take over the world. Likewise, Jared can be unleashed at any time and should the Malachai be "freed," Jared would be freed as well to fight him. No matter how bound Jared is, if the Malachai becomes a threat, Jared would be rallied to stop him. That's why Jared exists.