Haruo's ultimate sacrifice is based on his complex character development, which he undergoes during the trilogy. Haruo himself is representing the human nature without strings attached to it - while he starts as an angry teenager, willing to go to war against human-made monster, having gone through both the adamantly convinced Bilusaludo and the endlessly despairing Exif, he ultimately chooses to end the possible legacy of both by vaporizing the last remnants of Nanometal against Godzilla's plasmic breath. He commits this sacrifice so that the future generations of humans, now manifested in Houtua, live and prosper safely with the Godzilla as a reality. Without the Nanometal, Godzilla has no reason to become aggressive ever again, unless someone restarts the destructive cycle of irresponsible overtechnology.
The film's central theme is a call for harmony between technology and religion. The Houtua are the complete antithesis to the philosophies of the Bilusaludo (scientific extremism) and Exif (religious extremism). They integrate both into their culture; religion in the form of worshipping Mothra and being at peace with the natural order, and technology in the form of medicine, advanced underground civilizations, language, and writing. They are a rejection of the two extremes and represent a middle ground. Technological advancement isn't inherently bad but must be used responsibly, which is a theme that has been present since the 1954 original.
Once Ghidorah landed on Earth, Professor Martin and his assistants’ lack of ability to fully analyze and capture Ghidorah on their gadgets and devices shows just how horrifying Ghidorah is when he’s not bound to the laws of our world.
King Ghidorah emerges from a black hole. Now what exactly was blamed for the destruction of the Bilusaludo homeworld?
Whether you think Haruo's sacrifice at the end was heroic or not, he decided to do that because Martin showed him he could still reverse engineer the Nanometal technology and potentially pose another threat to earth. And now not only did Haruo leave a new family behind, but the good doctor is going to live with the fact that all of his closest comrades are dead and he indirectly convinced the last of them to kill himself along with the comatose Yuko. Esoteric Happy Ending, alright.
