In fact you didn't read my post properly. I only speculated on why Naofumi did what he did. I never said anything about my opinion on the need for the execution objectively speaking. They of course should have been executed for their crimes driven by pure greed (Malty) and abuse of power driven by irrational hatred and prejudice (the king), and for both of them collaborating with the pope for open rebellion.
However, ask yourself, does any of this need to matter for Naofumi? He's past the point of giving a shit after what he went through. If you had been betrayed and abused by a foreign country for a long time, would you feel the need to seek justice for the country? No, most likely you'd hate the country. You might like some individuals within that weren't scumbags toward you, but that's it. It would be natural to want dead the prime culprits, but if you hadn't turned into a berserk and still had the mental faculties to consider your own benefit for the future, you might as well do exactly what Naofumi did. Does it impair the bigger justice? It does, but it's not Naofumi's problem. This way he undoubtedly got the better deal for himself because the queen and Melty are thankful, plus it seems like the population liked his act of showing mercy as well.
This is kind of like accepting a big money compensation after being wronged by some powerful people, instead of seeking the case till the end in the court of law, where the people received a greater punishment, but you received less compensation. The people rotting in prison won't make your life afterwards any easier, but the bigger money compensation would have.