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.
So with all of these examples in mind (and feel free to mention any I might have forgotten) what are your opinions on this topic? Was Jake right, or at least justified, in doing what he did? Did he hesitate in #21 just for tactical reasons or because he had developed more of a moral compass since #6? Remember this would have happened not long after #19, when they first learn of "good" Yeerks. Was it justified in #6 but not at the end of the series?
TLDR: Is it morally acceptable to kill a Yeerk without a host?