Anyway, wern't the Andalites planning to exterminate Earth or something?
Yep, that was my point. The military was going to on their own accord. But the Animorphs set up communication with the Andalite civilian net, which, once that was revealed, is why they didn't.
If the military/government/ whatever, decides they can instill their will w/o the peoples consent, they're asking for an uprising, and they don't want to face off with their own people.
The issue of the Yeerk home world is never highly detailed, but unlike Earth, it's a reasonable bet that the andalite populace was aware enough of that situation that the military couldn't get away with moving in, doing it, and apologizing later. They'd never get clearance for either in advance, but if the Animorphs hadn't been able to say "we won, it's safe" the military may have been able to be forgiven for wiping out a primitive species that greatly would have empowered the enemy after the fact.
Yeerk probably would be more akin to a worm infection. Some worms may be able to suppress effects, but nothing is 100% immune to immunity. And keep in mind that worms have probably been evolving with host immune systems since time forgotten.
The body could still be expected to recognize a foreign entity, whole or disassembling, and should have some response. That the Yeerks can suppress this response from every potential host without prior exposure is either 1) ludicrious science fiction (most likely that) or 2) a marvel of nature, considering how different in methods this independently formed immune systems should be.