You might check out The Sparrow: A Novel by Mary Doria Russell. Here's the summary from Kirkus:
Brilliant first novel about the discovery of extraterrestrial life and the voyage of a party of Jesuit missionaries to Alpha Centauri.
Russell lays down two narratives: One begins in 2059, in the aftermath of the mission; the other in 2019, when a young astronomer intercepts a transmission of haunting songs from Alpha Centauri. In the latter, a linguist and Jesuit priest named Emilio Sandoz swiftly organizes a group of Jesuits and civilian specialists to turn an asteroid into a spaceship. The ship will reach the singing planet, called Rakhat, in four years of passenger time, even though 17 years will pass on Earth. In the narrative beginning in 2059, therefore, the mission's only survivor, Sandoz himself, is only a decade older. But he is a broken man physically and spiritually. The mission began well: Rakhat was beautiful and bountiful, and the men and women from Earth lived peacefully alongside a gentle and dreamy race, rather like the eloi of H.G. Wells' The Time Machine, here called the runa. Then, inadvertently, the visitors improve the local diet, causing a surge in births among the Runa; suddenly, another, fiercer race appears to put things right. It seems that the Jana'ata raise the Runa like rabbits. The newborn are slain and eaten, as is the party from Earth, except for Sandoz, who is taken to the strange capitol city and sold into a brothel. There, he is raped repeatedly by the great poet who wrote the angelic songs that fetched the Jesuits in the first place. A startling portrait of an alien culture and of the nature of God as well, since, in his utter humiliation and in the annihilation of his spirit, Sandoz is reborn in faith.
It's got a young single survivor on an alien world. I don't know about the pterodactyl thing or the shoulder injury or the caves. There's a strong religious component to the story, so that fits your recollection of Christian-ish. The cover art is blue, and at least one edition has the words "a novel" as you remember it.