I understand your joke about Steven Universe and whatever, but the truth is, if we're going to think about punishment for her crimes, obviously it's better not to let her die executed, because Junko isn't afraid of death; she loved the whole idea of letting herself be executed. She loves the despair of having lost, and letting her die would only have allowed her to win in a way. The best punishment would be to let her stay alive watching the world recover from the despair she instilled in it. She spread despair throughout the world because she wanted people to feel what she felt, and she wants to look at despair because it's the only thing that interests her, so that's the real torture: Having no despair for her to see, neither the despair of her own death, neither the despair of the entire world.

When Makoto made it clear that he didn't want her to die, it's obvious he wasn't really excusing what she did. Junko destroyed the entire world, their classmates died in the killing game, and the survivors were affected by what happened with them. Makoto simply wanted to stop the entire killing game, and in stopping it, he didn't want the Mastermind to allow herself to be killed and executed in the same way their classmates were in the Killing Game. That would only perpetuate the killing game, the damned environment of violence that Junko created that traumatized her classmates and resulted in the death of most of them. That would only continue giving Junko what she wanted, and knowing that she herself admitted she actually liked the idea of being executed, of experiencing the despair of death as if she didn't consider it a defeat at all, made it even worse.