Executing the Emperor would have led to the immediate shattering of the surrender and peace process. The Japanese would never have accepted such an action and it would have led to years more conflict and guerrilla warfare that would have made Vietnam look like a tea party. The United States did the right thing and the results are obvious today.
I agree that executing or imprisoning the Emperor would have been a mistake. But it was also a mistake to allow him to keep his throne. It just perpetuated the myth that Japan’s leadership was at some level innocent.
Hirohito should have been treated much as Kaiser Wilhelm II was. But keep the throne for stability reasons. Force Hirohito to abdicate in favor of his son.
If whatever leadership in Japan would not surrender, there would be nothing left to surrender. As the Potsdam Declaration stated, "We call upon the government of Japan to proclaim now the unconditional surrender of all Japanese armed forces, and to provide proper and adequate assurances of their good faith in such action. The alternative for Japan is prompt and utter destruction."