Does the Trolley problem apply here? (i.e. diverting the enemy from your town, if you know it is likely they will just attack the next town over) http://en.wikipedia.org/wiki/Trolley_problem
A competitive strategy could produce a net benefit for all the cities, because diverted bombers might be less likely to carry out an effective attack on their secondary target.
In fact, that's what happened in this case (assuming the smokescreen had an effect). By the time the bomber diverted from Kokura to Nagasaki, it was so short of fuel that it could only attempt one bombing run. Visibility was poor, and the bomb detonated off target above a valley, with the result that parts of the city were shielded. The death toll of 40-80,000 was 'only' about half that of Hiroshima, despite the bomb being more powerful
edit: The outcome could have been even better, because the orders for the mission stated that they had to clearly see the target. If not, they were to return with the bomb. Really, it sounds like they ignored these orders, perhaps because they didn't have enough fuel to carry the bomb back.