As a Christian who believes in the Bible, I'm quite open to questioning my beliefs and have no issue with fantasy - that is, the depiction of magic, magical beasts and the like. It's partly a way to test myself but also because I know what it real and what is not. Do I believe in ghosts and spirits? Not a bit. Will I watch a show with them in it? If I like the idea, sure. Then again, I'm pretty stubborn and my faith doesn't really waver because of that, soo... XD
(Also, I'm flexible. If science discounts a piece of my beliefs, then there must be something that I don't have the answer to in my religion yet. There's an explanation out there, I just don't have the facts to make the connection so I basically say 'Okay science. You and me, we aren't mutually exclusive. There's an answer out there that makes us both fit together so I'll just trust your truth and still believe in my truth too. I don't know it all but hey, you're the one with the degrees in what is. We can both exist at the same time, no fuss. There's some answer out there for it and I'm sure it'll be found eventually. Just gonna trust you and religion both for now.")
That said, there are a few games that I'm sure you can play though finding ones without anything fantastical in them will be hard. More modernistic games might suit you better, some sci-fi and perhaps ones that focus on human condition rather than religion.
Alter AILA might be worth checking out, from what I recall. It's sci-fi but I can't recall there being religion or any kind of ghosts since it was set in a dystopian future. Skills are based on weaponry, not magic.
I'd recommend Leo and Leah, but there may have been a section in there about a ghost (it's about lion cubs finding each other and is cute as anything!)
Hm... Castle Chase is a dating simulation where you're a princess who meets different people in your home castle. It's innocent enough to pass the Christian test.
There's a lot of puzzle games around. Pengui follows a penguin through icy puzzles and it's cute.
Crazy Vet and Zero's Impossible Fortress are two other decent puzzle games.
Oh, Sunset Over Imdahl is a must! It doesn't deal with religion or spells or anything of the like... though there is time travel. Hm... I'd still recommend it since it's one of the best games out there.
Pirates: Legend of the Silver Crescent would be okay, too. Pirate penguins in search of treasure. I don't recall there being anything supernatural within.
To be frank, I think that knowing magic isn't real and recognising that is enough. You know it's not real, a game isn't going to change your mind about that. :/