No. They had hundreds of years to find a way to protect Academia from whatever shockwave the falling cocoon would have caused. Also, they could just have dismanteled cocoon piece by piece instead. The plot is completely terrible and makes no sense at all, and that's it.

And no, Lebreau said those things what, three years after they left Cocoon? What makes you think they are experiencing those same problems several hundred years later,in a city that is several thousand times larger than New Bodhum?

You can't really make a city as big and prosperous as Academia if famine and monster attacks are still a real problem.