It's much better if the big Nankai Trough earthquake doesn't happen.
It's best if the big Nankai Trough earthquake but never ever happen
It's much better if(〜方がいい) the big Nankai Trough earthquake(南海トラフの地震) doesn't happen. (起こらない)
It's best(幸い) if the big Nankai Trough earthquake(あの南海トラフの地震) does never ever happen(が来ないと)