This is a book with an interesting perspective, pity it is too long. The basic thesis is that Christian faith pushed aside Greek rationality aside for more than a millennium, until Thomas Acquinas finally reconciled faith and rationality again.
The first one third of the book, the best, attempts to demonstrate how the Christian faith is a collection of beliefs from various sources. Only a small but obviously very important part of the Christian faith has come to us from Christ through the gospels. Paul was another major source for Christianity, for example in his hostility to sexuality and in particular homosexuality (about which Christ seems to have said little). A third source were the four oecumenical councils in the fourth century which settled on numerous detailed and often formal questions, such as the theory of the Holy Trinity. In many cases the Roman emperor had to intervene between squabbling rival factions within Christianity to take decisions in religious issues, subsequently ratified by the Church fathers, more on the basis of political expediency than on any other basis. The consequence of this pyramid of sources is that, although the main principles had been formulated by Christ - most notably, love thy neighbour -, Paul and the early Church have added so much to this body, that Christ might not have recognised his own faith by the fourth century. And it gets worse.
Christianity moved in two directions. Firstly, following the proclamation by Constantine, turning Christianity into the State religion of the empire, the Church became materialistic, in contrast to its early roots which emphasized poverty and abstinence. In some ways this is reminiscent of what happened with communist parties, many of which probably started with the best intentions, but soon the party degenerated into an institution which was used by its leaders to gain wealth and prestige while at the same time the original beliefs became dogma to beat up heretics. Freeman does not focus on subsequent reactions to the materialism of the Church (from within the Catholic Church, starting in Cluny, and by Protestantism).
The second direction of Christianity, the move away from Greek rationalism to a belief in miracles and making science subservient to faith, gets most of Freeman's attention. Augustine comes in for most of the blame : he advocated an unquestioning acceptance of faith and believed that rationality - and therefore science - was a threat to the true faith. Augustine was perhaps the most influential figure in Christianity after Paul, so when we look at the Middle Ages and see the Church fighting science, people believing in superstitions, persecuting witches etc... more than one and a half millennium after Aristotle advocated rational explanations for every phenomenon, we have to blame Augustine to a large degree. Augustine - and the Church - borrowed heavily from Plato who believed that body and soul were separate worlds and that the soul was paramount. This implied that knowing about the material world, i.e. science was unimportant, if not dangerous.
Freeman cites the example of astronomy, where the last recorded observation by the Greeks was by the Proclus in AD 475, after which there are no recorded observations for over a thousand years, until Copernicus in 1543. A similar gap exists in many sciences.
Contrary to Plato's teachings, Aristotles' books had been lost in Europe until the renaissance and in fact came back to Europe through Islamic philosophers in Andalusian Spain. (A graphic illustration of this crucial period in Europe, the break between ignorant and superstitious Middle Ages and the rebirth of Greek rational thinking, when the Church was desperately trying to prevent the subversive translations of Aristotle and other Greek philosophers from spreading, can be seen in the film In the Name of the Rose.)
The Christian philosopher who finally reconciled rational thought and Christian faith, and whose theories were largely accepted by the Church itself, was Thomas Aquinas, as such perhaps the most influential person in the western world after Aristotle himself. According to Thomas, rationality was not to be feared, because it would strengthen faith. This meant that after more than 1000 years of hostility to science, the Church suddenly accepted science and rationality. It is ironic though that only a few hundred years later, many scientific discoveries would undermine established Christian dogma and indeed threaten if not the faith, then at least the Church, but by then this movement had become unstoppable.
Given the huge impact on Western history and culture of the Church's attitude to science, I think this book paints a very interesting perspective. I do not think this book is blaming the Church of today; it merely illustrates that until Thomas, Christian faith for over a thousand years had been Platonic, with an emphasis on the soul and a rejection of rationality, but the Church itself quickly embraced Aristotle's rationality following publication by Thomas of his Summa Theologiae.