That is definitely one of the plot holes in the book. It's handled in a very simple game-ist way where the heroes are basically choosing their final boss battle by killing someone last.
As you and I are both running with a 5th cult (mine being a secret to even the leaders of the cults) that raises the possibility that the prophets themselves are mislead. That's what I'm going with. I'm probably going to map out multiple outcomes depending on what the characters can possibly do.
The campaign books default assumption is that all 4 cult leaders are squashed and one elemental prince enters our world but is then destroyed. The four elemental nodes are shut down. The weapons are used to shut down all the nodes. More than likely the elemental prince that is killed is just set back for some time (do elementals die if killed on the material plane? I didn't think so, but I am uncertain). This is actually a pretty neutral ending. The characters have stopped the cults and the eye "for now". They've set back the individual elemental princes goals "for now". Sure, the valley is saved, but the entire adventure didn't change the game world. You are heroes, certainly, but what came of it?
My likely "bad ending" would actually require that all four princes are summoned and destroyed on the material plane. That was the Eye's plan all along. The cultists summon their respective princes who are in direct opposition and go to war. Since the cults have been pitted against each other and the princes are always destined to go to war with each other, the original plan was to weaken all of them. Then the double agents from the greater cult turn on their respective wounded masters with artifacts (the motes in my game) designed to steal their power. That power would then be used to bring something out of the eye for a real world ending problem. Obviously the players in my game have messed up this plan already by acquiring the motes, killing a prophet, and setting back (and unbalancing) the whole plan. However...
The "good ending" in my head at least at the moment is that if the players intentionally summon and destroy each of these elemental princes, use the motes for their own purposes (the motes are bound to one of the PCs right now), they can purify the weapons that were granted to them (uncursing them, granting new powers) and eventually mount an attack on the creature behind the Elder Elemental Eye. Big ideas. No idea if I'll ever get to that point. Doing this would "actually" change the game world somehow. No, "We'll get you next time batman."