Look at it this way:
1. Mirai and her crew can't prevent the Americans from building the B-29
2. Mirai and her crew can't stop the Americans from seizing the Marianas
3. Mirai and her crew can't stop the Manhatten Project.
4. Mirai and her crew can't prevent the B-29 raids on Japan
4. Mirai and her crew can't prevent American submarines from unrestricted warfare against all Japanese shipping. She may be able to stop some in her immediate area of operations, but that doesn't help areas away from her. And her effectiveness as an anti-submarine platform drops considerably, once she runs out of homing torpedoes.
So, because of the above, Japan cannot prevent B-29 raids over Japan, the firebombing of Tokyo, or either of the atomic weapons on Hiroshima and Nagasaki. As for number 5. once the IJN runs out of fuel, Mirai and her crew are probably stuck in Kure, out of missiles, awaiting the constant bombing raids from B-29s and the US Navy. It could get even uglier than it was IRL, especially if Japan gets a nuke and uses it on the Americans. The resulting American fury would ensure the total destruction of Japan. So much for their "saving more lives".