The difference between Kefka and Kuja is that Kuja was completely sane and in control of all of his actions when he commited his vile deeds. Kefka was nuts. He couldn't help it. It's like the difference between premeditated murder and temporary insanity. One is downright evil, the other is uncontrollable and habitual. That's not a justification for Kefka's deeds. He was still an evil threat to the world, but it certainly makes him less consciously evil.

In addition to that, the awful acts Kuja commited were far worse than anything Kefka ever did. Kefka set Figaro Castle on fire, Kuja obliterated Alexandria. Kefka enslaved the Espers and drained them for their magical powers, Kuja created the Black Mage Race, enslaved them and made them murder one another. Kefka re-arranged the face of the planet, Kuja destroyed a planet. Pound for pound, Kuja was the more evil of the two. The things he did were more damaging, more violent and more heartless than anything Kefka did, and he did them all consciously and willingly. Kefka was a victim of psychosis.