In my opinion, if the history of the world says that the good gods commit acts of genocide and get to still be labeled as "good", then the history deserves to be upended.
From a worldbuilding perspective, Of course the gods that committed the cataclysm would want to be labeled as good. You're always the hero in your own story.
Plus being labeled the "good" gods is much better from a branding PR/recruitment angle. So yeah, those are the "good" gods, after having won the big conflict in the past. So since they won, they're definition sticks.
Now, if you're doing a world hopping campaign with some kind of truly "universal" war between good and evil - things get interesting.