I believe it was the Emperor who wanted to surrender, in fact he was trying to surrender to the Russians (which is stupid) before the bombing of either city but his cabinent members were not 100% in agreeance with it. The offer of surrender to the Russians(again, stupid but they were already on the ground in mainland Japan making their way south) was carried out in secret due to the cabinet members(involving the whole overthrow thing I do believe). I did an essay on this in college and used several reports that were made by our Government after the war that pointed to an invasion of Japan as highly unlikely due to a possible surrender by Japan. But then again my brain does not exactly work as it used to anymore so I might be completely wrong on that.
Very true on the fire bombing of Tokyo. Many, many, many people died in those attacks.
Either way, it was the only thing we could do at the time with the knowledge we had. It was the safest bet.
ETA: As I was, they attempted to use Russia to communicate to the allies for a peace talk, not to surrender to them. I will try to find the original documents if anyone is interested.