While I don't agree with the argument that Yeerks are evil, I do believe that they were antithetical to the existence of humans. They are the invaders. We never asked them to come here. We have every right to kill them and get them off our planet, whether it's one at a time or millions at a time. Now, I agree, there may be some innocents on there, there may be some that didn't want to enslave or be in the war, but that is on Visser 3's karma tab, not Jake's.
If the humans decided to start a war with another planet, mixed a bunch of civilians in with all the warriors and sent them to the planet on a ship, and the inhabitants of that planet killed the ship in self defense...is it the other planet's inhabitants fault that civilians died? Nope, that's humans for being stupid and cruel enough to put civilians in a war zone. Jake had every right to defend his planet and win the war. It's not his fault Visser Three had civilians on that ship.
While the argument can be made that some people liked having a Yeerk in their brain, they were still enslaving us. Like I said above, if I develop a case of stockholm syndrome, it doesn't make it right for you to enslave me. I know some Yeerks had a change of heart WHILE on earth, but that doesn't give them any more right to be here. That's like a burglar coming in, setting up shop in my house and forcing me to be his slave, then him going. "Man, that kind of sucked. My bad. Well, I'm gonna stay here, but maybe I'll try to get some burglar convention together to try and get all the burglars to be nice to the people they rob of their lives." Um...yeah...that's nice...but GTFO of my house...lol.