Atomic bomb

Yes, but remember they didn't mention the Emperor one way or another in the Potsdam Declaration. I believe the more savvy politicals on the war staff, certainly Togo, saw this as meaning that keeping the Emperor was not out of the question, especially since the Declaration did call for the removal "for all time of the authority and influence of those who have deceived and misled the people of Japan into embarking on world conquest" Not mentioning anything about the Emperor was seen as an opening.

One thing that is interesting was a remark made by the Navy Minister Yonai Mitsumasa stated that the atomic bombs were "gifts from the Gods" for ending the war. He was afraid that if the war continued that the Japanese government would be overthrown by military hotheads. A near coup actually did take place during the interim between the decision to surrender and the actual surrender.

 

The US was in all effect back then, ignorant of Japanese customs and the meanings behind words and how they're used.

It also must be said that while the Japanese dillied and dallied, many people were still dying. And the war had to end. It was no ones fault but their own that the bombings were required.