Killing god is indeed a major theme, it seems that every JRPG ends with you killing god with the power of friendship, doesn't it? Even in Persona 4, that's the true secret ending, almost as if the game is saying, "alright, we have to do it."

Definitely not an obsession with kabbalah, haha, though that is creative anon. Not a reaction against Christianization either, because this colonizing force was exterminated in the Shimabara Rebellion and the development of a State religion took the form of State Shinto, which, although inspired by State Christianity policy, was not influenced by Christianity at all and merely sought to codify and standardize Shinto (fundamentally a pagan, syncretic, folk religion) much like scripture does for Christianity. The Japanese see Christianity, today, as supremely exotic, even sexy at times.

First, let's look at Japanese religion, Shinto, because it's very different from Christianity. Much like early Christianity (it may shock you to learn that this is true, haha), in Shinto, one may become deified, may become a deity. This means that a human has the potential, by whatever feature of their character or even simply fate, to become godlike: to give a Chinese example, look at the poet, author of the Li Sao, Qu Yuan. Multiple historical and pseudohistorical figures are likewise deified in Japanese religion, some of the most popular deities belong to this realm, such as Hachiman, who is indeed a deified Emperor Ōjin.

Second, Japanese deities die. Izanagi kills Kagutsuchi, the god of fire, because his beloved wife-sister Izanami dies of burns giving birth to it. The food goddess Ukemochi/Ugetsu-hime is famously killed to make crops, a Japanese variation on the Hainuwele-type myth whose mere presence in the Japanese archipelago has immense ethnographic implications. And so on, the kami aren't gods like the Christian god or even like the immortal Olympians or the Sumerian pantheon, they are deified persons, natural phenomena, even objects - Amaterasu's girdle of magatama beads is itself a kami, per example. The Murder Of God, then, does not have the same implications of metaphysical impossibility to the Japanese.

As for the emperor renouncing his status as a kami in the Showa period... I think if anything, the taboo of going against such an embodied representative of the State would make this type of ending/theme in JP media even more pronounced. To rage against God, to the Japanese conception merely the kami of kami, the supreme kami, a representative of the current order in all its manifestations, is to rage against the current order, which, again turning to the Japanese context, means the endless disillusionment of the post-80s bubble economy and its suicidal work-culture, the total loss of sex and intimacy in Japanese culture (look up those virginity and sex-having rates lmao), the grind of school-life that is replaced by a much worse grind in the workplace, etc. The Emperor is (symbolically, not in fact), the State, and the emperor was a kami. To rage against god would be to rage against all of these, embodied in god, and if he was still a kami, in the emperor by association.

In short, to the Japanese who come from the background of Buddhist-influenced Shinto, to kill God is to go against a set (miserable) fate, to remove divine backing from the current order of things and to go against the "Status Quo" in the most vaguely defined embodiment possible - He who Created It.