The Last Starship from Earth — John Boyd

The novel is set in a dystopian society in the very near future. Although it is not obvious at first, this is also an alternate history story. The central character is Haldane IV, a mathematician, in a caste-based society. He forms a forbidden relationship with Helix, a poet. He also becomes interested in investigating Fairweather, a famous mathematician who lived shortly before his time, and his son Fairweather II, whom he discovers led a rebellion, which was defeated. Eventually he is given a show trial and deported to another planet, where he meets Fairweather II. In this world, Jesus Christ became a revolutionary agitator and was never subjected to crucifixion. He assembled an army to overthrow the Roman Empire, and established a theocracy that has lasted until the twentieth century. He was killed by a crossbow while entering Rome, so the crossbow becomes a religious symbol similar to the cross in our time-line.