It would pretty much be an unanimous decision from the military which is basically in complete control at this point and yes it would be fully possible. Would be no different from the night of the long knives. Just redefine the narrative and get rid of anything inconvenient. As long as the military remains in control, anything the emperor decides is meaningless. The emperors opinion in 41 is whatever the military wants it to be. The japanese were loyal to the idea of the emperor and not the emperor itself.
yeah dude Admiral Yamamoto is probably not in Tokyo most likely he is out at Sea right now and is quite well protected and will most likely get some communication from Fleet headquarters about what has happened. considering prime minister Hideki Tojo had made more than enough enemies within the Navy.
and a attack on the Imperial Palace by the Japanese military before the Emperor is even buried. Japanese people at this time we're loyal to the emperor you're talking about the government the Japanese government used him as a puppet and made people Revere him as a god and now they're desecrating the gods home after his death the people who actually believe that he is a God would go nuts
regular Imperial soldiers cannot enter the Imperial Palace for obvious reasons like what is going on right now so there is no sneak attack where the Japanese military simply March in and take over the palace. Tokyo is flooded with people coming to pay their respects to the emperor I don't see this night of the Long Knives you've talked about happening as smoothly as you're thinking
once the Japanese Imperial Guard repeal the first few attacks which they will because no sane Japanese officer or anyone within the military would dare use artillery or explosives on the Imperial Palace. people within Tokyo will start showing up. Japanese civilians attacking soldiers attacking the Imperial Palace Soldier start shooting civilians this isn't Nazi Germany the Emperor is a religious figure as well as leader of Japan.
God forbid someone from the media with the help of civilians and possibly members of the military take control over a radio station and broadcast what's happening. you got yourself a civil war right there.
you can say the a Japanese military accuses the Imperial Guard of killing the emperor but that would be like throwing egg in their face considering some of the most notable generals of the Japanese military were members of it. not to mention influential Japanese families that have their children in it.