Well that was oversimplified to say the least...
They had no defence because Japan's air capabilities had already been mostly destroyed.
There were little reprocussion because you know, it was a member of the Axis that was being nuked. Wich nation would go on a crusade to defend Japan against anything at that point? Maybe if youd like to be marginalized and associated with the falling Axis you would.
Now, how the world would react if, say, URSS started a nuclear war on the cold war days? Do you feel there would be no reprocussions, and that they would get away with it with just a slap on the wrist?
It may not be necessary to go further, I think you get the point, but you could also say : Why didnt the US drop nukes on Vietnam long before it got out of hand ? It surely would have been a much cheaper and quicker solution to the war.
There are serious reprocussions to using nukes...there are reprocussions to BUILDING nukes. But given the circunstances, these can range from warnings to DoW's. It would definitly be interesting if the game could mimic this using what the game has to offer.
Political statements\references used in the below post are being made to highlight game mechanics, lets not derail the thread into a geopolitical\historical debate more than necessary.
Oversimplified perhaps, but still accurate. The US droped two atomic devices on a country that was incapable of defending itself and the world barely blinked. If we're going to talk about realism as well as introducing unhappiness penalties in the game, then we're forced to look at the only real situation that we have on record. Regardless of Japans allegence at the time, the majority of the world didn't care and the US suffered very little unhappiness. But that came from a social point of view where people didn't question their governments as we do now, perhaps the discovery of Mass Media could introduce unhappiness for Nuclear weapon use, but if your nation has been at war with someone for 4,000 years and you level one of their cities, I'm not sure how upset your citizens would be. Not very is my first guess.
With regard to the USSR, I think you'll find that the majority of the world doesn't actually support a western point of view. During the cold war, the USSR had many allies all of whom wouldn't have been greatly upset that Washington DC was slightly flatter than before. So we're left again with the game mechanic of diplomatic penalities, which could only apply to Civs that had a sufficent level of friendliness with the victim Civ. Quite frankly if the Mongols and the Aztecs are at war with the Babylonians, why would the Aztecs get upset that the Mongols nuked Babylon? Just as Bejing wouldn't get very tearful if Moscow nuked New York.
Your comment re: Vietnam raises an interesting point. Perhaps we should consider that in 1945 only one country possessed nuclear weapons, by 1955 that situation had changed and the nuclear standoff was in place with the weapons themselves operating as a deterrent against their use rather than the show of strength they previously were. In fact as demonstrated in the Cuban missile crisis, they had become more political tools than actual weapons (although barely half an hour seperates us from a very different reality I admit.)
However, the Vietnam war wasn't a war between two nations, it was more-or-less a civil war that the US decided to take sides in to combat the "threat" of communism. I doubt that the South would have been too chuffed about their brothers in the North getting nuked regardless of the poltical agenda and thus the US would have utterly lost support and effectively handed South Vietnam to the communists. Civ, as far as I know, doesn't have a mechanism to replicate this situation, although I get what you're driving at.
Lastly, in the modern world, due to a certain government believing it can police the world, the building of nuclear weapons does cause issues. And it is this part that I actually like.
There is a modifer already for Civs which dictates their inclination to use nuclear weapons. There is also a notification for the Manhattan project that lets you know the other guy has the capability to use them...
What if.....if both sides have the Mahattan project, then they recieve notifications\information regarding the number of nuclear devices. A player is less likely to attack a Civ which has a nuclear arsenal and the AI can have it's modifer adapted depending on the ratio of nuclear weapons between the sides?
Thus, you have a functioning nuclear deterrent.
(If you don't have nukes you're screwed, but lets face it, if you've only got a spear you're pretty screwed against a guy with a handgun too.)
) Even disregarding safety mechanisms, any crash is going to be violent enough to render the atomic bomb's detonation sequence inert - again, you'll just end up with a localized environmental hazard. 
