In Japan's mythology, gods can be killed, this isn't the western Judeo-Christian "omnipotent" variety of god. Think of them more like ancient polytheistic deities, like the Greek or Egyptian Pantheons. It's very plausible that they are actual gods in terms of the Ancient Worldview. I mean they turned themselves to stone and yet were still "alive" and affecting the world. There power is also enough to tear the surface of a planet apart when it's just seeping out of them unfocused. In truth, we never actually do get to see the full potential of the Warring Triad since their first awakening is simply the overflow of their power being knocked out of balance, and later Kefka is only using part of his power to torture the world.

Part of the issue here is that the Woosely script kind of screws things up, because his script mentions that their are other beings like the Warring Triad, where as the Japanese and GBA scripts downplay that entirely. Simply stating the Warring Triad feared each other's powers and went to war. As far as they are concerned, they are the only three sources of magic. Magic could only return in a sequel if it was revealed that there was more beings like the Warring Triad and if they possessed the power of magic as well.

Honestly, I feel that would cheapen the whole story of VI if a sequel came out and it just involved a new Warring Triad showing up and making humanity repeat another War of the Magi. I actually really like the finality of VI, in terms of being a fantasy story.