While the Emperor was still considered a literal God at that point he did begin to lose slight influence with the military leadership towards the end when his inner circle convinced him seeking peace and surrendering was the best possible outcome for their Empire. There is still much secrecy in the communication between the Emperor and his military leadership especially prior and after the dropping of the atomic bomb on Hiroshima. Many reports show that the top tier brass of the Japanese military knew of the bombing up to a day before however never issued any orders of evacuation or really any orders at all. After Hiroshima the Japanese propaganda machine was in full force basically covering up the entire incident.

Many on the inside knew surrender was the only option even before the first bomb and Japanese agents were sending correspondence prior to Hiroshima to the United States seeking terms of surrender. However the US would not agree with their initial terms of surrender allowing the Japanese to keep their current "Imperial Way" of government with the Emperor still in place as their lord. This gave the military leadership the proof they needed to harden down on the stance of no surrender.

While I believe the Emperor could have wielded ultimate authority early on and forced his military leadership to accept surrender based on the Potsdam Declaration it is hard to say for sure. While disagreement may have been in the open at time I still believe the military leadership were unwavering in their loyalty to the Emperor for the most part but you have to understand for them surrender was the most dishonorable way to the leave the war.