This was a deliberate political decision in an effort to not repeat the grave mistake of how post-WW1 Germany was handled which essentially led to WW2. Denying Japan of their identity and dignity would have risked an eventual WW3, and the US did not want to even entertain the possibility.

It also didn't help that practically all of Japan were not going to see their Emperor deposed or worse; Japan was willing to compromise on literally everything but the Emperor in making peace with the US and the west, and the extended Imperial family along with all the other nobles thereof lost their titles and powers in the post-war occupation and restructuring.