To be fair, it was a decision based on many factors. In comic time, the Cataclysm wasn't very long after Contagion. Add to that the fact that Gotham is one of the most corrupt cities in DCU America, and the fact that it is filled with some of the most dangerous nonmetahumans in the world...
I'm not saying that the leadup to NML wasn't full of fail, but they tried to cover their bases with that particular plot point.