Christianity was absorbed into the state mechanism by the Roman Emperors starting with Constantine. One of the main issues with early Christian doctrine was how convoluted it was with numerous competing doctrines in the Middle East, North Africa, as well as East and Western Roman Empire.

One of the political problems for the Emperors was maintaining public order and all the different Christian groups and their in-fighting over creed could negatively affect that order and the Emperor's ability to govern. Consequently the Emperors would step in, announce a Council, and then stack the council such that a state backed 'orthodoxy' in Christian was found. Later Emperor's would even pass law that would brand Christian doctrines outside of the orthodoxy as heretical.

Constantine also bound Christianity into the arm of state through making the Churches tax exempt. As a result Bishoprics became wealthy places to run and Bishops took on political aspects; maintaining their power and wealth in the empire through becoming a vessel of state policy. Bishops sought to maintain the status quo through orthodoxy in order to maintain their tax exempt and wealthy positions.

Alongside this was the philosophical difficulty in explaining the relationship between God and Christ through reason. The Greek method of though was slowly replaced by the domination of faith over empiricism and the world became less scientific and more mystical as a result. The political use of faith as certainty and truth was also used to subdue reason. The Bishop of Milan, Ambrose, in replying to a Western Senator wrote:

What you are ignorant of, we know from the word of God. And what you try to infer, we have established as the very wisdom from God.

So we have a religious order, trained in politics and wealth by the Roman Empire in order to maintain public order, and with a doctrine that places certainty and truth in the wisdom of God and backed by the state as the common 'orthodoxy'. With the collapse of the Roman Empire into West and East, the political power of the Church in Rome was able to replace a weakened Roman state in Rome. This process arguably started with Pope Leo who began to establish the Holy See as the dominant political power.

More than the toppling of reason to faith, it is rather a story of Christianity as a political movement and the ease with which it could establish and maintain its political power through the doctrine of certainty in faith.

* As a note, I would probably give Peter Freeman's book a miss. I wouldn't read it again. It was interesting but confusing and the thesis wasn't so obvious in the second two thirds of the book.