There was widespread indignation when the pope recently let his opinion on British equality law be known. Now, it looks like the churches will have their way. But is this a victory for ecclesiastical power? Well no, not quite. The incident was indicative of deeper changes in contemporary society. Few, as yet, have grasped quite what's at stake.

One person who might have is Harvey Cox, the distinguished Harvard scholar of religion. His new book, The Future of Faith, is a big picture account of Christianity and the point at which we've arrived today. To understand the significance of that, he argues, you have to go back to the beginning.

The first Christian period, following the death of Jesus, he calls the age of faith. It was one in which Christians, still fired by the original energy of their movement, followed "the way" that Jesus had taught – freedom for captives, concern for the poor, liberation from the grassroots. This period, roughly the first three centuries, was characterised by hugely diverse theological speculation as to the meaning of it all, witnessed to by relatively recent discoveries of non-biblical texts like the Gospel of Thomas. Hence too Saint Paul, in his letters, is not concerned with ecclesiastical uniformity but writes for particular churches, with the aim of discerning what is right in specific situations.

The age of faith couldn't last, and the conversion of Constantine marked the full commencement of what Cox calls the age of belief, the second phase. If the early Christians had worried about how they should respond to Jesus, it was now the turn of powerful prelates to control their flocks. Creeds were devised, heresies were defined. A long transition began in which believers had not only to trust in God but obey bishops too.

The age of belief lasted many centuries: hierarchical churches are strikingly robust institutions. Though the contradictions inherent in this period – between the spirit and the letter of the law – meant that it could not last forever. The Reformation marked a new turning point, which is still flourishing in what Cox calls the age of the spirit. It is, in a sense, a return. It nurtures a Christianity once more characterised by enthusiasm and diversity, and a distrust of dogma and hierarchy. As Cox puts it, "Religious people today are more interested in ethical guidelines and spiritual disciplines than in doctrines."

Now, Cox's book is broad-brush. Scholars will question many of his assumptions. Didn't the formulation of creeds not only serve to police boundaries but also preserve the ultimately mysterious nature of the phenomenon of Jesus? Is he right that Christianity's association with ancient Greek philosophy was detrimental, as it's now being recognised that ancient Greek philosophy was itself primarily about ways of life, not systems of thought, too?

But his snapshot of the contemporary religious scene is unapologetically taken from the mountaintop, and it is also unapologetically optimistic. Cox recognises the risks associated with some of the features of the age of the spirit – its fundamentalism, say, or the prosperity gospel. But he argues they can't last. They are essentially reactions against modern biblical scholarship, which means "a religion based on subscribing to mandatory beliefs is no longer viable". Hence the emphasis on the spirit. Neither does he worry that Christianity today so often feels like a Jesus-centred personality cult. Rather, Pentecostalism is a positive force, part of "an inexorable movement of the human spirit whose hour has come".

So what's this got to do with the pope's recent intervention? Episcopal hierarchies are too taking heart in the observation that God is back, to use the title of another recent book exploring our religious times. However, what Cox suggests is that this title is, in fact, misleading. It's not so much that God is back, as that multiple versions of God are back, even within apparently monolithic churches. The age of the spirit is an age of anarchy, not uniformity.

Hence, in the Catholic church, at least in the west, few take much notice of Catholic sexual teaching, but pursue essentially secular moral codes instead. Conversely though, Catholic social teaching is becoming very influential in Britain. It forms the ideological basis of thinkthanks such as the Centre for Social Justice and Res Publica, which could play a big role in government should the Conservatives win the next election.

The plurality of the age of the spirit is, therefore, one that hierarchical churches, moulded in the age of belief, will find increasingly difficult to control. "It is the truth revealed through scripture and tradition and articulated by the church's magisterium that sets us free," wrote Benedict alongside his remarks about the equality legislation – he being the articulator-in-chief of that magisterium. However, the future of faith is going to be a painful one for prelates, if Cox is right. They'll have to become accustomed to controlling fewer of the levers of religious power.