Well in this story, they want to keep it secret, because such an event would cause mass panic. Franklin and the Negative Zone, among other easy fix-its, aren't available in this story because it would be the easy way out; which greatly diminishes the emergency of this situation. Also, there's the part where they want to stop the problem entirely. If they've already excused themselves from the problem, what's pushing them to try and stop a problem which no long affects them, their Earth, or their universe?
People have to realize that the exclusion of all these easy outs, makes the story much more interesting and compelling.