I don't know about whether any government figures died, but the answer is that the districts targeted by the firebombing did not include the Emperor's Palace, Tokyo was very large, and despite the fact that many people died, far more people survived.

Here is a map of Tokyo from the time that shows population density. You can see that the Emperor's Palace is distinctly visible in the center. The areas heavily bombed were those dense areas to the east, along with the docks, which, as you can see from this map were also the most flammable areas of the city. The fires did circle around the area of the Emperor's palace, but the palace itself was sufficiently set back from the rest of the city that it acted like a firebreak.

In terms of your likelihood of surviving, Tokyo was a city of some 6 million people. The dead from the firebombing raids was around 80,000–100,000 people. So that's a death rate of 1-2%. That's a lot of death, to be sure! (As we've seen from the "only" 1% who have died of COVID over the last two years, which adds up to millions of dead.) But it's small in terms of percentage. Even in terms of mortality per area, it's about 5,000 people per square mile destroyed. A huge number — but again, your chances of surviving, if taken as just random probability, were still high.

By comparison, the atomic bombing of Hiroshima was 3X that mortality per area rate, and Nagasaki was 4X that rate, but the total number of people in those cities was less, so even with very high death rates, the numbers are less than Tokyo. If you kill a small percentage of a huge number of people, it will still be a very large number in absolute terms.