Mary Doria Russell's Children of God.
From Amazon.com: "Children of God is the sequel to Mary Doria Russell's 1996 The Sparrow, which saw a Jesuit mission to the planet Rakhat end in disaster. The sole survivor of that mission, a priest named Emilio Sandoz, returned a beaten and broken man, having suffered rape and mutilation at the hands of enigmatic aliens. Now the Jesuits want to go back to Rakhat, and they want Sandoz aboard the new mission. But Sandoz has renounced his priesthood and even found a measure of happiness with his new wife and stepdaughter. Meanwhile, on Rakhat, contact with the humans has thrown the local culture into turmoil, precipitating a war between Rakhat's two sentient races. As forces conspire to send Emilio back to Rakhat--and toward a possible reconciliation with God--the planet verges on genocidal destruction. Children of God is a more polished novel than The Sparrow, and the story is equally compelling."
More polished, I disagree. I actually found this book sort of boring. It dragged on and on, and I almost didn't finish it because I kind of didn't care. But since I loved The Sparrow I thought I would finish it. The most interesting thing about this book is that the coy I got from the library was sort of falling apart when I got it and in the end the last 20 pages and the back cover flew off while I was on the subway-it was sort of embarrassing.