Look at Western Civilization. Slavery is somewhat of the same premise as what the Yeerks did. The Yeerks just did it better.
And to your point about Visser One attempting mass forceful infestation, not EVERY SINGLE YEERK agreed with that plan.
The My Lai massacre of 1970 is a bit like this. The American Army under Nixon THOUGHT that everyone in that village supported the Viet Kong, but that wasn't really true... it was a village of civilians. All killed. The Lieutenant was charged, and only served a couple of years, but there IS a precedent... its sort of the same thing.