Animorphs is of course famous for its moral greyness. The Yeerks are colonizers unquestionably in the wrong, but the Animorphs are not given a pass to just wipe them out: not only are there Yeerks who have tried to change the Empire from within, and even some who have created a symbiotic relationship with their host, but they are also a group separated from their home world with no where else to go, since any attempt to return will mean being killed by the Andalites.
The Andalites, despite being the Animorphs’ allies, are self-righteous xenophobes operating under a propaganda military government that hides from its citizens its war crimes, including the attempted genocide of the Hork-Bajir. They only care about killing the Yeerks because they see the Yeerks as their fuck-up: Seerow gave the Yeerks technology on the misguided belief that they would cooperate and go on to better things as allies, so now the Andalites want to wipe out their mistake. They don’t care what other species fall as a result, and they certainly aren’t in a hurry to prioritize Earth.
Even the Animorphs’ other allies, the Chee, aren’t given a pass in their pacifism. Everyone knows the Chee could end this war in like a day if they would alter their programming. But the Chee have proven they don’t really care about humans; they side with the humans against the Yeerks so they can save humanity’s closest companions, dogs. And we also learn that they protest too much when it comes to their pacifism: when confronted with the species - the Howlers - that killed his creators - the Pemalites - Erek learned that the Howlers were in actuality nothing more than literal children, being sent to other worlds by the Crayak to wipe out civilizations but only thinking it a game; and Erek intentionally withholds this information, hoping the Animorophs would wipe out the Howlers regardless, despite knowing they were technically innocent, so he wouldn’t have to dirty his hands.
And even the Animorphs themselves have blood on their hands. They learned early on - were in fact told straight up front by Elfangor - that the Hork-Bajir are an innocent, enslaved species. They later meet freed Hork-Bajir, and the species is heartbreakingly humanized again and again. But even as the reader empathizes with these characters we come to know, the Animorphs continue to treat their species as collateral damage. They will try to go out of their way to avoid killing human controllers, but Hork-Bajir are still justifiable kills to them, because they are so dangerous by design. But this doesn’t excuse them. Toby and the free Hork-Bajir are never allowed to be completely forgotten, so we the reader are never allowed to see the Animorphs’ slaying of the Hork-Bajir controllers as anything glamorous.
So many children’s series fall into the romanticization of war when writing about kids going up against The System (whether it’s an invading alien species, the government, The Man, etc) but the Animorphs has consistently held onto its anti-war messages well, deconstructing the genre of “kids save the world.” The Animorphs are never given an easy answer.