Just a few bad examples? It sounds like the Yeerk Peace Movement was just a minority. Most controllers were murderous thugs. I highly doubt that it was only a few Yeerks taking the others 'against their will' that decided to take over the world.
I like to think that an equal comparsion can be found in Nazi Germany, like RYTX said. The Nazis had a corrupt, murderous system of government that condemned resistance, so of course the image of the Nazis today is that they were all evil, right? Well there were even members of the Nazi party who tried to assassinate Hitler, and there were certainly members of the general German public, even if it was a minority, who thought what their government was doing was wrong. Some Germans tried to help save Jews and other people threatened by the Holocaust. They're still human, and they're capable of disagreeing with something that they grew up believing was right.
Like I mentioned before, the Yeerks and all the other major alien species in the series were very multidimensional; not all Yeerks were murderous thugs. Maybe not even most. In fact the Yeerks were peaceful on their home planet for most of their evolution, until the Council of Thirteen decided to blow that pop stand and start taking over other sentient beings. It seems like lots of Yeerks wanted to become nothlits to escape the war, or help humans fight against the Empire (that Yeerk who was helping break people out of cages in #53), or fight against the Empire themselves (the Peace Movement). It's my personal opinion, because the Yeerks were portrayed as alien but with all the drawbacks that any human might have, that it isn't fair to characterize them all as evil just because they grew up surrounded by propaganda that told them it was their right to enslave other people. That so many Yeerks fell in for that (and why wouldn't they, they're doing what they're born to do) makes them very human and very sympathetic in a sort of tragic way. The fact that Yeerks still decided to go against everything they grew up believing and put their lives in danger to help members of an alien race makes me think that some of them are willing to do whatever it takes to stop the war, and make some peace with the moral dilemma of taking other people's lives and bodies.
*deep breath* XD; As for the against their will part, of course Yeerks have a choice not to take someone over, it's just that if they're told to do it and refuse they face death or suspicion as a host sympathizer (which is a death sentence, anyway), and if they aren't told to take a host they're forced to live their lives blind and helpless. What would you do in that situation? It's as if it would've been better if the Yeerks had never known what they were missing. Ignorance is bliss, right? The fact remains that most Yeerks weren't involved in the rebellion against the Andalites, most of them were just whisked away from their homeworld, probably without even knowing about the resistance or maybe without knowing about the Andalites at all. Then these thousands of Yeerks were given military orders, from their leaders, to become a part of an invasion force on other worlds. Sure, some of them probably loved the ego trip and the power. I just find it hard to believe, given the evidence over and over again of some Yeerks simply wanting peace, that so many of them were anything other than brainwashed into believing they were right to take over other worlds.
We can agree to disagree, right?