Humans couldn't stand the presence of ants and insects in their homes, and similarly, Agatha felt the urge to get rid of humans for they were ants as far as her power was concerned.
In the end, every lifeform was an ant from the perspective of a comparatively superior being. There was no concept of good or evil involved. It was just plain instincts to not care about the life of a weaker form of life.
The urge Kiba felt was countless times stronger as his entire 'Kiba' form was created by the Cosmic Spark. Every single cell in his body was powered by the cosmic force, unlike Agatha who only inherited a single cosmic particle.
Her source of power was both Divine Particles and the cosmic particle, so the urge for getting rid of 'annoying pests' was comparatively weaker. The other factor which worked for her was that she only felt this urge when she used her powers.
