Is it too edgy to have a protagonist commit despicable war crimes and his arc is learning not to be guilty but rather to embrace his actions?

I'm not sure you can easily sell that to anyone. You might find a readership for a brazen and uncaring MC, but I think the majority of readers have a moral compass that is going to whirl at this justification.

If you took him from guilt, through justification, into coming to terms in a way where he took responsibility for the choice - perhaps recognizing that he had to do it but also bowing to the horrific loss of life, or the value of life, or any redeeming viewpoint that could come from such an experience - then I think you'd have an easier time of selling it.

I believe there is virtue in owning one's decisions as much as in learning to live with no regrets, but to never take any responsibility for a horrendous crime, and to boast about it and never feel any sense of its brutality....I don't think many people are going to find this character redeemable in the end. And that's going to really anger your readers.

I think that readers will create allegorical ties to historical events like this, which are usually considered horrific atrocities.

Also the incident as you have described feels kinda reminicent of corrupt police officers killing unarmed people / people who have surrendered and that is a really controversial topic lately.

I guess my point is most people will probably not empathize with a character who learns to forgive themselves for doing something like that. Maybe you could have him attempt to make up for this by helping the aliens like the end of Ender’s Game or something.