Going back to the original question...
I imagine that certain Yeerks were perhaps allowed to morph sentient beings, and I imagine it would often be a collaborative agreement between Yeerk and host. The actual act of forcing all Yeerks to nothlitize would be a huge undertaking, but assuming that the humans and Andalites have control over the Yeerk Pools on Earth, not impossible. Those that did not show up in three days would have three options:
1) Die
2) Be lucky enough to have their own portable Kandrona supply
3) Resort to cannibalism - a short-lived solution at best.
I imagine that upon entering the Yeerk Pool, Yeerks would be required to leave their host permanently and the host would then be interrogated to see if they have any Imperial sympathies. I don't know what would happen to the voluntary hosts, but I imagine that they would be treated and tried as war criminals.
The Yeerks would then remain in the pool indefinitely as the Andalites and humans began the nothlitizing process. This process could take months, as they have to not only convince the Yeerk to accept the morphing power, but also the body that they are being given. I think that some group of conscientious objectors would realize the implied genocide, and as such a small percentage would be allowed to morph human. The rest would be given harmless animals with reasonable life spans, and those that refused to morph would be killed.
One of my roleplay characters is actually loosely based on this concept. I imagine a post-war world where those Yeerks who obtain human bodies permanently are treated as sub-human, and sent to camps not unlike the Japanese internment camps of WWII. Their children, or "grubs", while being fully human and having never known what it was like to be a Yeerk are treated equally poorly and ostracized from mainstream society.
I imagine this would allow for a lot unrest, among both the nothlit population and the human population. Rebel groups would form, fighting for nothlit rights and effectively creating a very volatile situation.
Can't tell I've thought this through, eh?