I have never quite understood why the Japanese hate Christians so much that even in random fantasy/isekai manga villains very often belong to a religious order that reminds the reader of the Christian church outwardly, like with a cross as its symbol. Christian missionary work in Japan was quite inefficient and more or less ended with the central government slaughtering and torturing most of the Christians to death. After that it played no role whatsoever in Japan. By the WW2, it was the political play of superpowers that resulted in the Japanese dream of controlling the whole East Asia to crumble. Most of the American troops might have been Christian, but it was of little consequence in the modern world of 1940's anymore.
I can't really think of anything but cowardice behind it. Christians in the world won't typically attack a novel/manga publisher with assault rifles if an insulting work is published. The author doesn't need to fear car bombs or even a simple knifing.
As a secular person I don't much care personally, but I do find it intriguing.