There were two main reasons.
The first is that this would have created significant political difficulties. While Japan was occupied, it was never occupied with sufficient force to continue a long guerrilla struggle against a resistant population. Hirohito’s continued involvement with the American occupation meant that it could be conducted peacefully.
The second is that Hirohito’s actual ‘guilt’ was a bit questionable. While he was inarguably aware of what was going on, there were sharp limits on what he could have done about it. While not quite the figurehead of the English monarchy, his power was primarily moral or social rather than direct. He didn’t directly control any major sector of the economy or military force. Almost all decisions of the government were made with his tacit acceptance rather than at his direction.
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