Could be a BIG problem...
Question: I am a really firm believer in being true to the characters in one's story, and writing the characters as you think they would act as opposed to writing them in order to please everybody. My problem: A certain character in one story I'm writing is probably going to offend a LOT of people. My story is NOT Christian literature, nor does Christianity play any large part in the story at all. In fact, the moment in the story I'm about to mention is an "isolated incident" of Christianity; Christianity's cameo in the story, I guess. Anyway, this character is neither the hero nor villain, but he comes really close to the anti-hero role. He does what he can to support the hero as they are best friends (in fact, the hero is this character's ONLY friend), but he is not at all what most would call a "good person". He is reclusive and cold-hearted, and doesn't see much point in concepts like mercy or compassion; In his eyes, if you were stupid enough to wrong him, you deserve a full punishment. But the core of his character is a near-universal disgust of modern society, by which I mean he can't stand how a few customs and ways of thinking (e.g. Christianity and industrialization) have more or less taken over the world (polytheistic religions are gone, "Western culture" is spreading like wildfire). In general, he just sees the modern world as bland and bigoted in contrast to the diversity Ancient World. In the one scene I mentioned earlier, a pastor tries to persuade him to "accept Christ", and offers him a crucifix pendant. Having such a personality as his (part of which is a burning pride in his own polytheistic heritage), he takes great offense and spits on the pendant in the man's hand before walking away. It is perfectly true to this character... but do you think it is a bad idea?
Let's look at it another way.
say you were writing a book set in Germany in the 1940s and Adolph Hitler was a character. And let's say you were going to include a scene representing the moment when Hitler ordered the mass killing of the Jews in Eastern Europe.
Would you, as a novelist, stop and say "Oh, that's too evil an act to include in fiction. Instead, I'll tone it down and just have Hitler refuse to invite some Jews to a dinner party."
In other words, would you become a Holocaust denier and shield your reader from the historic, if ugly, truth?
I don't think you would. And if you did, I don't think you would be doing your readers a favour, especially those who were underage, because you would be giving them a false understanding of history and human nature. I don't think the majority of your readers (who are mostly smart people) would praise you for it either.
Now, I don't know what message you intend to convey in your story. I don't know if ultimately you are on the side of Western culture or against it. I'm certain you could make a convincing case either way.
But I do believe you have to be honest. If that character's actions ring true to you, then that's what you should write.
If there are good reasons why your character hates Christianity, show them. Present his feelings, thoughts, and history around this issue. Give even the most devote Christian reader what he needs to say "Well, I don't agree with what that character did, but I understand why he did it. It was true to life."
If you can do that, then all will be forgiven. (Making people think is part of a writer's job.)
On the other hand, if this character is meant to be a villain, you should still give the reader a glimpse of why he is the person he is. Villains with understandable reasons behind their actions are far more interesting and effective.