Not straying too far off topic, my main point was that Jake should be better than that.
I don't see his decision to kill all those defenceless Yeerks as a military/tactical/strategic move. Your main argument focuses purely on their fighting potential which is valid only if they were already armed and were pointing guns at you. I would support your argument by saying I would destroy the enemy's weapon transport or war machines BUT the key points are that 1) those specific Yeerks in their current condition were as helpless as baby children and 2) their deaths held no purpose other than for Jake to release his anger. Even Cassie couldn't quite say their deaths was a distraction. They might not be innocent but you wouldn't shoot a child would you? 100 children? 17000?
In wars there are rules of engagement. As the most responsible leader for the Animorphs he knows this better than anyone. In this particular case Jake blatantly threw those rules out for his own selfish feelings.
If you say it is wrong to kill an innocent in war, than it is IMPOSSIBLE for then to kill any Yeerk at all. When you kill a 'non helpless' yeerk, an innocent being is dying, whether it is the yeerk or the host. Saying that it is wrong to kill an innocent, in this case, is like giving the Yeerks a free pass to walk all over us. A host is more helpless than a child, they cannot even control their actions while a child can. It would be immoral for Jake to wait until they became "un-helpless."
As long as they were in orbit above our planet, they were trespassing. They should not have been there, and that makes them an enemy combatant. While I understand some of the Yeerks may have not wanted to be there, again, that is not Jake's problem.
Even if Jake did it because he was angry, I do not fault him for doing so. Anger is a justified emotion in a war, whether it was anger at Erek or anger at the Yeerks. He had every right to be angry. Asking him not to be angry in this case is like asking someone to not be angry if you came home and found your house gutted and ransacked. Even if we digress from that and say his anger was not justified, that can be separated from the act. If I am not mistaken, this was the
act that ended the war. Even if Jake's motives were suspect, the act itself was not wrong. (In my opinion.) He prevented the infection of 17,000 of his own people and ended a terrible, bloody war. I don't care if he did it because it made him giggle, the act itself wasn't wrong.
I personally do not believe them being in a helpless state gives them a free pass to be trespassing on our planet, and I consider in orbit above us trespassing. We have a right to shoot down whatever is on that ship, because that ship is there to ultimately invade us. Those yeerks are intended to enslave us, it isn't right for Jake to sit around and wait until they have taken a helpless life. Would it be wrong for the Yeerks to shoot down an Andalite ship from orbit to try and free the quarantine? Well, what if there were Andalites napping on that ship? They are helpless. Are the Yeerks obligated to board the Andalite ship, go "hey, everyone wake up and be not helpeless! Actually, here's a couple dracon beams so you can shoot at us while we go away so we can get you out of property in good conscience," and then somehow get off and blow them up? No, that's silly and stupid.
Again, it is sad that there are innocent civilians on that ship. However a) it is physically impossible for them to sit there, sift through them, and find out which ones are civilians and which ones aren't. Especially since if held at gunpoint I'm willing to bet every single one of them would be "innocent." And b) it is not Jake's or the Animorph's responsibility to babysit the morality of the Yeerks. If 17,000 burglars poured into your home and said "hey, we have no guns, we're helpless," does that give them to trespass on your property? Nope. It sucks that they may not have had a choice to go into your home, but again, that's not your fault, it is your right and your
responsibility to protect your property.
Also, for the prior analogy about a foreign species killing 17,000 humans if we were trespassing on their property, IMO, they would be completely justified in killing us if they did not want us there. We are invading
them, it is their choice what to do with us and how to deal with us. We put ourselves there in a place we should not be, anything that happens to us is purely our fault.