I enjoyed Narnia, but found His Dark Materials unbearable. It's been a while since I read it, though, don't remember the specifics. The soul mate with animal spirit thing just seemed Christian to me - stunned that it is supposed to be an atheist book, as another comment mentioned.
So I am not opposed to religious art. A bit tired of the "chosen one" theme in fantasy, but other than that, I tend to just view it as an expression of human yearning.
One thing is what the author puts into things, another thing is what the reader gets out of it. Animism and spirits is hardly limited to Christian mythology. I personally thought it was kind of clever and vivid imagery, especially with the mad scientists fuelling their doomsday device by ripping children apart from their souls, much like splitting the atom lead to horrific suffering when used as an engine of war - or much as certain dogma in education seems engineered to squash the imagination of children.
At any rate, I can absolutely accept that the work didn't appeal to some as much as it did me - but I just thought it strange that the reason should be that it was somehow particularly "Christian". Strikes me a bit like ignoring the parallels with the story of Christ and eg. that of Horus/Osiris. I'm not convinced people didn't come up with the stories about virgin birth, magical manipulation of water and so forth without having to hear another version first: the point is more that if you have a character that's born from a virgin, that doesn't have to mean you're trying to invoke an image of Jesus Christ. Although, often, it does mean just that.
Then there's the issue of universality of myth (sacrifice, kindness etc) - and from a certain set of religious views one could probably argue that any "atheist" myth is simply anther way for a deity/deities to make his/her/their will known...
But it's different things to include religion, which is just stuff people believe, and actual souls. Religion is just a belief. Churches are just companies.
But I admit, in that sense any fantasy novel containing magic might be "religious" in some sense. The soul thing just seemed rather Christian to me.
I am an atheist and not that well versed in Christianity, though.
So I am not opposed to religious art. A bit tired of the "chosen one" theme in fantasy, but other than that, I tend to just view it as an expression of human yearning.