I can see how this would upset some people, but I suspect that most of those people wouldn't read, since the story obviously has a religious theme from your header, so anyone who was sensitive could avoid it easily.

I like the idea that L is mildly disturbed by Kira's attempt to set himself up as a god, and that such thoughts would wander into topics like the falseness or not of other religions and other deities, and the blame games played by worshipers.

As to Christianity in Japan, the only things I know about it is that it is quite small, often looked down on, and often thought of as magical and mysterious by outsiders (sort of like the pop culture view of Voodoo that Americans have). Christianity is big in Korea, though.