It looks like you missed an important point. Just like previous replies said, killing Ryoji would only makes the cast forget The Dark Hour and delaying The Fall. Yep, delaying, not getting rid of it. And when the time comes, all of humanity including what used to be SEES will die cluelessly. This is why it is labeled as "The Bad Ending", and the ending where the protagonist sacrificed his life to completely stopping The Fall and preventing another coming of The Fall is labeled as "The Good/True Ending"