Didn't they worship him as a god? In fact, wasn't it that god worship that gave them the impetus and the confidence to overule their superior officers time and time again.
So it begs the question that if said god then told them, directly, to stand down, how could they get around it?
You misunderstand the nature of the role the Emperor played in Japan.
The Emperor was not politically relevant (had any real power) for over a thousand years at that point. He was a FIGUREHEAD only. The actual powers who controlled Japan (the Shoguns). Even during the Meiji "restoration", the Emperor did not have any real power. He just gave cover to the actual modernizers who overthrew the Tokugawa and ruled Japan. The real leaders of the Meiji Restoration was an oligarchy of powerful men lead by the "Three Great Nobles" of Saigo Takamori, Okubo Toshimichi, and Kido Takayoshi.
Presenting proposals to the Emperor was mere formality. He was expected to "approve" anything put to him.
Any real influence the Emperor had was informal. He could make his wishes known, and people wanted to accommodate him. But that did not mean they allowed him a veto. At best, he could help sway indecisive or softly aligned members of the ruling clique when there was a close dispute that could not be resolved (which was his role at the end of the war to sue for peace).
As others have mentioned, the most likely response to the Emperor demanding the military leave China would be a soft coup where the "bad advisers" who "mislead" the Emperor were removed, and new guardians appointed who could make sure the Emperor did what they wanted.
You seem to
misunderstand the nature of the Emperor's "divinity". The Emperor was not considered to be a supreme supernatural being who must be obeyed in all things. The Imperial family wasn't considered merely mortal or mundane. They did have a divine nature in Shintoism. But so did lots of things - places, animals, rocks, rivers. So the Emperor needed to be treated respectfully as he was part of a sacred order. But that was all.
If Hirohito defied the military and ordered them to quit China, it would create a very uncomfortable situation. But the end result would not be the people with guns meekly obeying. It would be to "restore harmony" between the government and the Emperor by eliminating the troublemakers leading the Emperor astray.
That people were willing to die for him is no different than that people were willing to die "for the flag". The Emperor was a SYMBOL of Japan and its people just like flags were to many people of all nations.