Very true, and very good point --
And perhaps a way to combine both outcomes for the author. Then it's not the MCs making the choice to kill, but the justice system reaching a natural, in-world conclusion.
Ah, this is very interesting! In which case there are definitely historical models that come into play.
Capital punishment following a trial might be a possibility for some of your antags, whereas others might be spared for showing remorse or for having a lesser role in atrocities committed (a la Nuremberg, which did result in death-by-hanging-or-firing-squad on multiple occasions, as Domi rightfully pointed out).
Something else you could take a look at is Reconciliation (capital R) in South Africa following the end of apartheid. I'm not South African myself and studied it relatively briefly (thus, don't want to say too much because I'm not super well-informed), but its aim was to heal and reconcile bitterly, deeply divided parts of their country by 1) holding those responsible for apartheid accountable and 2) bringing citizens who supported / participated in it back into the fold.
While I wouldn't model fictional events directly after IRL wars (and the fallout that followed), they might give you a little more background ideas re: a possible range of outcomes.
Butting in here to add that, even if there is something wrong with it ... sometimes it takes drafting it out and showing it to others to work out where the problem is. There's nothing bad about rewriting a chapter where your original idea didn't work!
I think sometimes we find it hard to give ourselves permission to try things that might not work. At least, I find that to be true in my case.