User blog comment:Omega natsu2/Chapter 368: The Third Seal, Predictions./@comment-4933386-20140120162841/@comment-7418318-20140120165155

On that I have two theories:
 * Theory 1: Zeref was so powerful that no one could stop him, so the mages at the time might have thought that living without any magic is preferable to Zeref dominating the world. Shortly before Face could be finished, Zeref disappeared and was presumed dead or asleep.
 * Theory 2: Dragons need magic to survive. Because they were suppressed and didn't have any way of harming the Dragons directly, the Humans came up with the idea of destroying magic, which would indirectly kill the mages. Living without magic is better than being dominated by Dragons they thought. Shortly before Face could be finished, the Dragon Civil War broke out, giving the Humans the hope of gaining their freedome without having to forsake magic, so they decided to wait.

Due to the catastrophic results of the weapon, they sealed it up and kept it secret in the highest echelons, but kept it intact and usable just in case the threat against which it was build ever came back.