Probably no surprise to see religion rearing its head in Prince Caspian, is it? C.S. Lewis's conversion to Christianity is one of the more famous instances in an already famous author's biography, and his Christian apologetics like Mere Christianity are pretty famous themselves (not Narnia famous but still). So it makes sense that Prince Caspian contains many parallels to the Christian religion. Aslan represents Jesus Christ, Peter and Caspian represent knights in the European Christian tradition, and Lucy's struggle with faith is a quintessential Christian struggle. For some, including J.R.R. Tolkien, this amount of allegory will be a little too much. For others, it'll be just right.
The Telmarines aren't given a religion of their own, making it difficult to read the war as a conflict of religious interests.
Peter and Susan's exclusion from Narnia definitely has religious undertones—especially given Susan's controversial fate at the end of The Last Battle.