I say it depends on who it is we're targeting, and how much military value his death will gain us. If we have bin Laden, or Saddam Hussein, hiding in an apartment building with 200 people, then those 200 people are toast. If it's some Hamas stooge, perhaps not, but it really does depend on what value we get out of killing him.
It also depends on what our relations are with the country. If we're formally at war, then blowing up that apartment building to get some one of military significance becomes much easier. In a wartime situation, the leaders of the country are committing perfidy if they place (or even allow) military targets in a civilian environment, and the blame - legal and, I believe, moral, for the civilian deaths is on their shoulders.
In the more likely case where it's a terrorist hiding in an apartment building in an otherwise neutral country, it becomes more difficult, and we're much less likely to blow up the whole building. However, as I'm sure you're aware, our sensitivity to civilian deaths encourages unfriendly nations to place military targets in civilian environments. If we wish to spare future civilian deaths, we may have to get over this, and start targeting military targets even if numerous civilian deaths are inevitable.
In the specific case of the article - Hiroshima - we were at war with Japan. Hiroshima was a valid target, but we killed a lot more civilians than was necessary. It is certainly questionable as far as the morality of that strike is concerned. In retrospect, I think it actually improves. The bombing of Hiroshima and Nagasaki ended the war before the Soviets got involved. For all the horror those two cities endured, it is truly minor compared to what would have happened in a North and South Japan. Just look at North Korea for a shining example.
Drew Garrett