At the time of 6, the Yeerks were regarded as always chaotic evil. I don't really remember how many were killed. If it was a lot, or just a dozen or less.
Tehn as the series goes on, they realise that maybe all Yeerks aren't evil. That maybe some of them are just trying to live normal, happy lives.
Tehn late in the series, everything goes downhill, and Jake isn't being himself. so he tries to rationalize flushing that huge pool into space.