The ethics on killing Yeerks while in their natural state (ie. without hosts and therefore helpless) is something that is brought up on multiple occasions throughout the series. Strangely enough, it's almost always from Jake's POV. Here are the main examples: (SPOILERS for various books obviously)
1. During the Andalite Chronicles, Elfangor strongly objects to Alloran's order to murder a large of defenceless Yeerk prisoners by flushing them into space. Despite everything he has been taught about how evil the Yeerks are and the importance of obeying his superiors, he effectively commits mutiny to save his sworn enemy because he knows what Alloran wants to do is wrong.
2. In #6 Jake casually boils a whole bunch of Yeerks in a small Yeerk Pool at the hospital, shortly before he is infested. He doesn't hesitate or show any sign of guilt over the decision and nobody objects to the plan.
3. However, a similar opportunity presents itself again in #21 during the David trilogy, and Jake is much more hesitant. He isn't necessarily concerned about the moral consequences, but realises that leaving the Yeerks alive is a better tactical decision, so that the Yeerks don't suspect the Andalite bandits have infiltrated the building.
4. And finally the big one: in the series finale Jake is once again faced with the decision on whether or not to flush the main Yeerk Pool aboard the Pool Ship. Again he is hesitant and is tormented with guilt afterwards, but in the moment he was angry and desperate and did what he felt had to be done.
Book 34: A Yeerk Pool on the Hork-Bajir Homeworld gets drained. Cassie feels remorse for that one.
End of Book 52: The Animorphs blow up the main Yeerk Pool, killing large numbers of Yeerks. Cassie appears to feel bad about that one too.
