I homebrewed my own setting that's set in the Italian Republics of the Renaissance, for which aspects and institutions of Christianity are in play. IMO it's best to treat this idea via Historical Fantasy set in an era and location where Christianity was the primary religion. And most importantly, let your audience of players drive the approach you take to evolving a campaign and telling stories. It also worth remembering that a setting in which one real world religion is dominant, could also offend players who are followers of other faiths which were historically dominated by the social strata and institutions of that prima religio.
If you have players that are followers of any faith that falls within the historical, cultural sphere of your setting, be mindful of that when you paint in the details and introduce conflict. I'd take the same approach for any prewritten, published setting that includes historical faiths, making adjustments where necessary. There's lots of narrative dials to turn and sliders to move when running a campaign that can change the way institutions of faith come into play. The reason I say historical fantasy, is because having elements of fantasy at the very foundation gives you as GM a bit more lattitude to tweak the narrative. You're after all tyring to present a world that players can enjoy roleplaying within, not a historical simulation game. Not that a historical simulation isn't doable, but IMO that'd take more consideration and care, and I'd most definitely have a zero session to guage the comfort level of my players as to how real world religions are present.
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