To be honest, it'd make a lot more sense to explain this as a Pokemon created disaster than simply a natural one brought on by the "Gods"
Not the beam itself, that can be branched off in many ways for a more interesting plot. But considering how the game involves Pokemon, a disaster created by one makes not only more sense, but leaves room for more improvement and less people to question the sense of the idea.
An example would be saying the god, or whatever you decide causes this, sends down "Emmisaries" to ensure its wrath is proved. The two control Fire and Ice, one making half a barren desert, the other freezing the land over.
To say the gods are angry over a fight as well is unrealistic. The title of a god, or deity of immense power is to deal with the world by NOT influencing it. To solve one problem with godly power brings people who rely on that power too heavily, thus gods do not show themselves or intefere with peoples lives. You could say that the two sides want to overthrow the gods however, similar to how humans tried to take over Olympus. The resulting anger caused from both sides caused the gods to seperate the islands and after time the two sides where formed, rangers and trainers.