Kuja started a major war, backstabbed the nation he sided with, destroyed Alexandria, and decimated a whole planet.

Kefka took over an empire, poisoned an entire kingdom, made the planet a dry wasteland, and became a God.

Sephiroth torched a village, killed a snake, killed a woman who actually needed to be killed to stop Sephiroth, and summoned a meteor which failed to kill anything, almost all of this under the control of Jenova.

I'm not seeing how him being his own demise stacks up to Kuja or Kefka's evil deeds. If anything Shinra was a far more evil than Sephiroth. Sure, you can kill them and end their suffering, or you can oppress them and slowly kill the planet.