Censorship of religion is nothing new in video games. It has been going on since the early days of Nintendo. I can name some examples.
Final Fantasy - Cross symbol above the clinic changed to a heart
Faxanadu - Crucifixion of Jesus as well as standard crosses removed. Priests renamed to "Gurus".
Splatterhouse - Level 4 boss stage changed from a church to a hallway with arches and altars removed as well as the boss itself changed from an inverted cross to a demonic face. In addition, the grave at the end of the game was changed from a wooden cross to a headstone.