Theory - Prometheus is actually an ally. Here's why:

[Sagaz]

First of all, we need to remember that one of the main themes of Hades 2 is the clash between gods and titans. It's not just about Chronos.

Several times we are shown how the gods have already done a lot of evil, such as Hades punishing Sisyphus, Poseidon (according to the game) lied about being the father of Polyphemus, Zeus gave eternal punishment to Prometheus, Athena punished Arachne and Hera punished Heracles.

Considering that Prometheus is now free and able to see the future, I believe he already knows that eventually Melinoë will defeat him and Chronos no matter what. Which doesn't seem to make sense, since he says he intends to be on the winning side. My theory is that, upon seeing the future, Prometheus saw an opportunity to trick Chronos (just as he tricked Zeus in the past).

But why is he fighting Melinoë, then? I speculate that it is with the aim of making her go to the surface and Mount Olympus, forcing her to face the last and unknown enemy, perhaps having seen that she could do it, but only if Prometheus was at Chronos's side, taking her to the real threat.

Furthermore, Prometheus must already know that the Fates are the key to stop Chronos.

Perhaps Prometheus is deceiving everyone with the goal of not only gaining Zeus's forgiveness, but because he saw that Melinoë is capable of perhaps making the gods care not only about the Titans (except Chronos), but also about mortal lives. Perhaps his goal is to try to stop the gods from being as arrogant, envious and jealous as they always have been.

Even Melinoë realizes that Prometheus and Polyphemus could have been on her side in the war if it weren't the gods' fault.

[★Miko]

Just like the reason why Zag kept running even though you completed the story already. Nice. I can dig that.

[StormRangerX]

I don't really remember if Hades changed the context of Sisyphus, but as far his myth goes, dude was a serial killer who then also screwed with hades and thanatos. I would say the rest of the characters you mentioned were definitely unjustly punished by the gods, but I'd have to object to Sisyphus being lumped in with them. He was certainly a chill dude by the time Zag met him, but that doesn't erase his actions.

[Kalir]

In the case of Sisyphus, I still wouldn't call the actions of the gods entirely just, because it wasn't all his other tyrannical behaviours that got Hades to hand down a parable-worthy punishment, it was specifically trying to cheat death. Sisyphus was still a terrible person (and the Sisyphus Zagreus acquaints himself with openly acknowledges that he used to be a terrible person and not someone to look up to) but it only became the gods' problem when he started trying to mess with their domains.

[StormRangerX]

Eh, even if you just talk about how he messed with the gods, him abducting Thanatos caused a lot of problems for everyone and his punishment was pretty thematically fitting. Compared to Arachne being turned into a spider for beating a god at a contest, or Prometheus getting like insane torture for defying the gods to bring fire to mortals, punishments that were a bit more in the vein of "the gods are being petty."