Interesting, and I believe it raises fundamental issues and questions. I'm not saying I have the answers but they provoke thought. Do excuse me if I make any mistakes - I know you're sharp on historical accuracy

1) The Japanese pilots acted 'on behalf' of the government of the nation where they were based. This raises 2 issues:
a) Evidence of the people responsible was clear, whereas in this case it was not immediately clear. It this time it is new believed we know who is responsible, but evidence is not in the public domain.

Bin Laden (assuming it is him) is an individual with an agenda. Granted he was supported/sheltered? by the Taliban government. Who do you take action against even if the perpatrator is known? It is acknowledged that the typical Afghan is not a target. Why was this different in Japan (i.e. Hiroshima)?
Was this because it was acknowledged that the Japanese people supported the actions?
Was this because the implications of retaliation were less (i.e. nuclear attack)?
2) This is going to be a provocative point. It's not meant to be antagonistic, just a thought.
In 1941 many nations were already at was with Japan as today many are at war with terrorism (The UK, Spain, Israel etc).
There is an argument (rightly or wrongly) that Pearl Harbour and the WTC incident stimulated the US into action, and that their interest in combating these pre-existing issues occured when they felt the impact directly.
Again I'm not insinuating anything - no flames please - just stimulating comment!!!