It is rare but present in some games, and initially was always viewed with neutrality rather than contempt because the Japanese as pioneers of this industry were respectful to the cultures they used to base their games off of, even if they tended to embellish with the Americanesque ones.
Some that I am aware of:
-While the Doom games are considered not evil because of slaying demons the entire time, there is way too much demonic imagery for it to be comfortable with a repentant believer who struggles with their faith and their walk. However, apparently Doomguy is a celibate Catholic.
-In Civilization VI one of the ways to win the game is by spreading Catholicism across the world.
-Kingdom Come Deliverance takes a somewhat stance on the Church, and many of the characters (NPCs) are priests.
-The early Castlevania series used a lot of Catholic imagery. The player can primarily utilize items like holy water, a crucifix (albeit Nintendo calling it a boomerang in the manual, but what it really is is pretty obvious), a blessed whip, and rosary beads to fight evil.
-Dante's Inferno is a bit of an imaginative take on the original Divine Comedy and there are some blasphemous elements within the game to those who can see it all, but it does make even the unbelievers fear hell.
-In the Dragon Quest game, the player saves their game by going to confession at a church, however the priest there can also revive dead party members.
-In Total War: Attila, as the Frankish faction, the player can convert to Latin Christianity, and then conquer the world building churches and monasteries everywhere.
The Joshua Graham character was genuine, and particularly because the game took place in the Mojave Desert and its neighboring regions, it would make more sense for the lore to have a Mormon in there than an Orthodox or a Catholic, unfortunately as it seems many unbelieving gamers developed a positive opinion of Christianity after playing this, but to have a fully fleshed out character exposition the history of the Church and such may have been too much and some (((executive))) may have shut it down.
The original envision for the Legend of Zelda lore was of a lone European knight saving his Aryan princess and her fair kingdom from the sorcery of a swarthy hook-nosed desert-dwelling occultist descending from a matrilineal lineage, while on a whole in the kingdom of Hyrule all the different races lived peacefully in parallel societies. No matter how much they've changed the symbology in the games evolution, these constants are always there. The original Legend of Zelda was deeply rooted with Christian references, including the "spell book" actually being the Bible. It was censored by Nintendo of America to avoid offending everyone religious and non-religious (go figure). The Japanese versions of the first three Zelda games have these Catholic/Christian themes. There is official artwork for "A Link to the Past" with Link praying before a crucifix:
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