Låter väldigt mycket som Gudsmotorerna av John Scalzi.
Från Wikipedia-posten:
The story takes place in a universe where space travel is accomplished by chaining intelligent, human-like creatures called gods to a spacecraft and torturing them to drive the ship. The people are ruled by an organization called the Bishopry Militant, who worship a powerful being. Captain Ean Tephe is completely faithful to the Bishopry, but his faith comes under test when he is assigned a secret mission which his ship's god seems to have a keen interest in
.