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I feel like either of those options can be done well. The character could also go back and forth for most of the story before coming to a solid decision. Or maybe he goes from being an atheist, to believing in a religion that isn’t Christianity and then realizes that religion doesn’t work and eventually comes to believe in Jesus. Maybe he’s searching for the truth, but ends up working through a lot of false worldviews before coming to Christ.

Another interesting thing that you could do with a story, is explore why the character believes what he believes. Is he a Christian because he doesn’t want to go to hell or because he wants a relationship with Jesus? Is he an atheist because he struggles with reconciling a sinful world with a good Creator or because it’s just what his family believes and what he was taught?

I think the author could make any of those ideas work. In the end, whether the story is cliche or not may be more dependent on how it’s written.