One of my more out-there fanon theories is that Krynn is actually a domain in Ravenloft, with Takhisis the unknowingly imprisoned darklord. Her curse is to continually try to take over the place but to be continually and almost accidentally foiled by a bunch of bumbling 'good' gods, a gaggle of emotionally disastrous adventurers who are continually distracted by their love lives, and her own hubris and squabbling minions.
That, to me, solves the Cataclysm Paradox. Why did the 'good' gods of Krynn commit such a monumental act of mass slaughter? Because they're not the good gods of Krynn, they're shadows wrought by the Dark Powers that act as Takhisis BELIEVES a good god would act...