But Shinto was repurposed to be about worshiping the emperor just a short time before the war - it had a long history and didn't have any bad ideology really tied up with it.

Hm? The central role of the Emperor in Shintoism goes back at least to the Heian era, and Shintoism was a critical tool of state power (witness the appointment of royalty to the most influential position in Shintoism, running the Ise Shrine). Or do you mean something else?