This is less about right or wrong but more about doing the best thing possible under their circumstances, less about the perfect thing, more about the best possible thing. It shows you how little control the hunters had agains the ants, they did not have the luxury of a perfect victory, only gon had a perfect victory for pitou.

Gon is not perfect, so he had to go through imperefect manors to get his job done.

Heres me trying to justify some of the things you are against:

A1.

Pitou attacked them first, they went in after seeing the other ants, which are basically psychopathic killers, they had not met any good ants until that point. Pitou could have changed this, but the show heavily suggests that she attacked more for enjoyment than for defense, you can also see that she has no remorse after killing him, she does not feel guilty, doesnt consider whether they are good or bad (more sad that she no longer has her play thing). In addition it's always the ants that attack first causing chaos to the NGL land, they give no space for dialogue to sort out their differences, they always go for the kill first then maybe beg after they have been completley beaten.

So Ants have no regard for human life, you can even see this in the scene when mereum and pitou go to that little girls village and murder/eat her, she cries, they even mute her audio to show how much fear she was in, to show that she cried in fear an cried but nobody heard.

Then all of a sudden pitou wants to save some random helpless girl, even though they have murdered hundreds before. I think GON hates this moral inconsistancy, he would rather you just say you are evil so he can kill you rather than someone who is grey, because then you have to justify killing them (which he does by showing her that she cares for this helpless girl but murders others, even though she cares for this girl, knows this feeling of care and need to protect, she does not consider that others might have the same feelings, so inherently she is selfish out of her own will).

A2.

Now this is a grey area, so if he kills pitou then he kills komugi, which at this moment GON is so emotionally unstable, filled with so much rage that he doesn't even consider komugis life (so was an easy choice for him). The question here is, does he kill pitou here and get it done with, or let this monster live, you know how powerful pitou is, she could take out all the remaining hunters. She is not like Youpi who has some form of honour, she will flat out kill everyone for the king. What is the logical solution here, to let pitou live so komugi can live, or kill pitou and potentially save countless other lives?

Gon was gonna choose, the logical thing and take out komugi and pitou, but killua convinces him otherwise, trusting that the enemy will keep his word. This ultimatley leads to GON being in the state he is and pretty much dying (fate worse than death) for komugi to be able to live, she fucking dies anyways so it was pointless regardless. So therefore it was ok to kill pitou and komugi there, its like the let the 5 people die by the train or switch the track and only let it kill 1 person. Logically speaking, it's killing the 1 person, of course some may say to do nothing, but would you let those 5 die so you can reject the guilt of being responsible for killing that one person?

A3.

Clearly GON has little emotional control, he was pushed to this state by pitou and the pressure he was under. People say they could have handled it better, but this was GONs first time experiencing such a thing like this, i think he handled it quite well. Alot of people would have just gon berserk if they saw pitou and had the means to kill her there (gon sort of did, but killua stopped him).