I'm not sure what bad governments have to do with genocide, but I am sure that allowing bad governments to exist falls pretty far afield from allowing a magical genocide that is basically a mass extinction event to be summoned by priests of Goodness. And one of them is pretty clearly the free will of the mortals in ugly action while the other is magically enabled by the gods.
What does feudal government have to do with free will? People don't choose to be peasants subjected to compulsory labour!
But anyway, as per my post upthread, I don't think the act/omission distinction carries much weight in the context of gods. If they're evil for killing people via the Cataclysm, then they're evil for not using their huge magical power to relieve all sort of suffering that they could trivially relieve. Conversely, if we make up
reasons why they can't do the latter - rules about non-intervention, or rules about respecting mortal choices - then we can make up
reasons why the former is not murder - rules about the necessity for punishment, and about respecting choices to do bad by inflicting appropriate retribution.
The Kingpriest + Cataclysm motif sits in the same general place as JRRT's downfall of Numenor. Both are about divine punishment for mortal hubris. Both involve punishment on a mass scale - whole lands sunk, destroyed, etc - because that is the literary device that conveys the point. Looking at these through a modern lens, in which collective punishment is eschewed and each individual life lost to the punishment is a wrong, makes no sense.
And, conversely, if that modern lens is going to be applied, then many of the tropes of high/romantic fantasy come unstuck.
Ultimately, it's like arguing that Storm is evil because she squanders her power fighting Magneto and Doom rather than relieving mass suffering. I mean sure, you can make the argument - Watchmen does - but then you're arguing to drop the superhero genre.
But if we drop the high/romantic fantasy genre then I'm not sure that there's much left of DL.