Most villains don't care about the lives of the people they kill, they see them as collateral damage at best. Kefka wants to be a god and goes around zapping people, Ultimecia kills everyone when she uses Time Compression, Vayne doesn't care about the people that get killed etc etc. Seymour does care about the people that is why he is killing them. The only reason Yuna and co. decide not to go along with the final aeon thing is because they have Tidus and Auron there. Tidus is from dream Zanarkand and Auron was killed by Yunalesca last time round so they have different ways of thinking about things.
Ultimecia didn't just want to kill everybody She wanted their existence denied. Which is truly evil. I agree with you about Seymour.