I seem to recall the main reason to even bother with that sidequest is so Strago can learn the Grand Train Lore spell.
Kefka's Tower was moderately difficult; the moon in FF4 and the Cleft in FF5 are both still harder. And what monsters did FF6 have to rival Omega and Shinryuu? Doom Gaze? Phunbaba? Blearghablahh. Who cares.
We only see the beginnings of a cleaned-up world after you send Kefka to hell. Wahhoohu-hu-hu!!!