I went back and read parts of #54, and it seems as though most Yeerks left the planet and were sent back to their homeworld, or they morphed--to what, it doesn't say. There's no mention of them when Jake talks about the rise of anti-alien terrorism, and I'd think they'd be the prime victims for attack by people who want aliens to leave the planet. So, it's probably all just guesswork figuring how Yeerks were treated, if any did remain on the planet. Wish we'd gotten some clarification on that
Early on in the book it's mentioned that four morphing cubes are given to Ax to do whatever he wants with (weird image of him trying to juggle them x3), so presumably Yeerks would be given access to one of these, to fulfill Jake's promise of allowing the morphing power to those who want it.
I still like the idea of Yeerks staying on Earth, especially as humans. Again, some of the Yeerks who might be considered trustworthy, like the Peace Movement members, might be allowed to do something like that. But most people probably wouldn't want one of them as their neighbor o.O;
Just human nature, I guess.