Well... a lot of these things depend on how you choose to interpret them. Yes, if you think that WC3 is merely supposed to justify Hiroshima and Nagasaki, then you may be right (if you can make a solid enough argument for it). However, movies and books are very often interpreted differently than what the author had intended.
Personally, I would say that WC3 does not attempt in any way to justify the bombing of Japan. The storyline never tries to persuade the player that destroying Kilrah is the right thing to do - only that it's necessary. In a way, rather than solving the moral issues people still have about the end of WWII, it asks those questions again, in a much more personal way. Instead of wondering about the morality of a decision that had already been made, you are forced to make the decision yourself.
Now, as for the Congress and other similar issues... yes, of course there is a certain tendency to make the game 'American'. You could similarly say that the use of the English language makes the game very pro-English. BUt both of those things are only to be expected, because it is a game which relied primarily on sales in America. On the other hand, note that this doesn't mean it's pro-American. Compare it with Independence Day, and you'll see the difference between slightly-Americanised and patriotically pro-American.