Religion has had a place in gaming for a long ass time, but in different ways.
Western gaming painted Christianity in a more pure light for a long time and the church as a place of rest, something Dragon Quest adopted since it exists in an old European setting where Christianity was responsible for people even being able to grow crops. Most JRPGs, however, usually use Christian stand ins as villains that act as good, having a more jaded view on the subject. They also paint the church as a puppet for a false god sometimes, like Mithos' plans in Tales of Symphonia. Sometimes it's just evil in general (FFX).
I like how Shin Megami Tensei deals with gods and mythology. These greater beings are only greater because they're stronger than man, otherwise they're just as diverse as people. The Christian God is seen as a trickster who gets people to worship him but brings order and a sense of peace, although he's also very unfair to those not with him (bringing to light the ideals of the Crusades). Satan is more of a force of pure chaos and freedom, but with no sense of morality. The various demons and lesser gods follow those that meet their qualifications, such as strength or simply an item.
I really like how it's handled in Persona 3 and 4.
These two examples feel human to me, flawed but understandable. I imagine if there is a god out there, it's similar in mindset, Just not as crazy.