This is Firebird by Kathy Tyers. If you read it as a trilogy, the odds are that you read the second edition, which seems to have a slightly different summary in Wikipedia than the first edition:
Firebird is a military pilot assigned to a risky venture to capture a Federate world outpost. Because she is a wastling, she is considered expendable. Leading her tagwing fighter group, she is captured by Federate colonel Brennen Caldwell, a telepath who senses something special about her. She attempts honorable suicide by poison for her failure, but Caldwell thwarts her medically. Under duress, her military knowledge is used by Caldwell to save the Federate outpost. Firebird begins to see the dishonorable tactics of her people for what they are.
Caldwell, in addition to being the most powerful Ehretan telepath of his generation, is also heir to religious prophecies among his people, and the most senior telepath in a government that mistrusts them for their abilities. Caldwell is promoted to general for his victory in the Veroh battle, as well as his diplomacy with the captured Firebird. In her, he sensed a strong possibility of connaturality, a deep personality congruity that is essential for telepaths to be married. As he has strong convictions against marrying outside his faith, and being barred from proselytizing, much of the book revolves around Caldwell trying to bridge the gap to Firebird by demonstrating the goodness of his spirit to her, offering life and hope to one who believed herself as good as dead.
Following Netaia's failure on Veroh, Firebird's sister Carradee ascends the throne after their mother commits suicide, a tradition within the royal family. She favors a conciliatory posture with the Federacy. Their other sister, Phoena, secretly plots the overthrow of Federate occupation along with members of the nobility, by secretly building an ecological weapon of great power. After several political and military dangers are overcome by Caldwell and Firebird, they ignore his orders and carry out a special ops mission to destroy Phoena's research lab. During the climactic battle, when Caldwell has been incapacitated and his telepathic powers are not available, Firebird casts her faith to the Great Speaker who sang the universe into existence, and strengthened by this, overcomes great odds to successfully neutralize the weapon.
The religious differences thus settled, the story ends with Caldwell proposing pair bonding (marriage) to Firebird.
Wikipedia also notes that the rewrite was also where it moved from Science Fiction Romance to a Christian Allegory.
My eventually successful search terms were science fiction trilogy captured pilot prophecy
