This was a scorched earth policy (kill all, loot all, burn all). Wikipedia mentions one historian, Mitsuyoshi Himeta, who claims that, but some internet and library searching has failed to unearth any other historian who agrees with him. My impression is that the claim is an explicit order, and I haven't been able to find work explicitly refuting that. Also, isn't the precise nature and role of the emperor unclear? I've heard contradictory claims and evidence, and like with a lot of other parts of history, it has gotten politicized and used as a tool/weapon for nation building and for points against others. As is usual, nationalists make me very frustrated. Some characterize the emperor as another evil person debating the final solution at the Wannsee Confeference, whereas others paint him as a victim like a bird in a cage. My impressions are that its a bit of both, as when the military coup happened, after the brief period of a pseudocompromise between the civilian government status quo and fascist military regime, the emperor was taken hostage for his own protection (reminds me Dong Zhuo during the fall of the Han Dynasty, and those stories were popular in Japan), and used as a symbol for power (mirroring the Shogunate?), but he wasn't an idol victim and was trying to negotiate and make the best of it, and had his own ambitions for himself and Japan, some of which didn't contradict and even agreed/overlapped.