Miyazaki's film has no responsibility to depict the atrocities in Nanking, or any other place in Asia. It is about a man who designed war planes, but he was not directly in control of how those planes were used. The only reason I would be angry is if the film demonized the countries at war with Japan (which doesn't fit Miyazaki's pacifistic attitude).
Nanking represented a horrible breakdown of military discipline, a perfect melting pot of horrible circumstances. A powerful racist military organization with zero accountability just took control of the enemy capitol after months of brutal, slow warfare. Many of them wanted revenge. However, when the slaughter happened, most of the people in mainland Japan didn't know about it. They were just told of the glorious Japanese military. The difference is that the slaughter in Germany actually occurred within their own country, and we forced them to acknowledge it. Japans war crimes occured overseas, and we were willing to make more negotiations with them in order to achieve a quick victory, before the Soviets moved in. None of this is really attached to a plane designer, who probably didn't even know about Japanese war crimes, and whose planes had little to no impact on massacres that were mostly committed by ground forces.
I think the issue is that most countries acknowledge their war crimes, even in the U.S. The United States imprisoned Japanese Americans and fire bombed civilian population centers. Russia... well, they were out for blood. The issue that makes people so irate is Japans refusal to acknowledge their mistakes because of their history strong ethnic central national pride. While I agree that this is certainly bad, and may have bad repercussions in the future, I'll repeat that this is a national problem, and not tied to Miyazaki's film in any way.
Off Topic: On a side not, I do feel compelled to play devils advocate concerning Hiroshima and Nagasaki. That really was the best option available at the time, as Japan refused multiple times to surrender. The military was prepared for a full invasion, and refused to surrender even after the dropping of the first bomb because they wanted to preserve their emperor. Some hokey historians have claimed that the Japanese wanted to surrender, and that we mistranslated a message, but this has been more or less debunked. The use of WMD's was a horrible event, but it also cost the fewest live. Several hundred thousand people died in the event. However, a land invasion would have costed an estimated 2 million Japanese lives, and 1 million Allied lives. More people died due to conventional warfare in Japan than died from nuclear weapons. The firebombings alone killed more people than Hiroshima and Nagasaki combined. Most people don't know that, though, because WMD's are a more dramatic psychological symbol, even though they killed fewer people. To make matters worse, a swift victory was needed, because if Russia had been allowed to invade from the north (they had already invaded Manchuria) then they would split Japan in half in the same way that Berlin was split in half. In conclusion, the use of WMD's was the best option in a bad situation, because it cost the fewest lives.
That said, the United States has committed war crimes throughout its history as well, including the destruction of Native American tribes, and the overthrow of popularly elected governments during the Cold War by the CIA.