Last week, composer James MacMillan's Sandford St Martin lecture was broadcast on BBC Radio 4.

It was entitled "The Divine Spark of Music" and was a provocative speech. He argued that music is the art form par excellence that draws its energy from religion and spirituality. In sacred music this becomes explicit, for the aim then is nothing less than to evoke an epiphany of God. He said:

I believe it is God's divine spark which kindles the musical imagination now, as it has always done, and reminds us, in an increasingly dehumanised world, of what it means to be human.

But the speech was not just a celebration of the "miracle of music", as Daniel Barenboim puts it. It was also a rebuttal, if not an attack. MacMillan believes that the fundamentally divine nature of music has been belittled in the modern age, not least in the cultural climate typified by the new atheists. What he called the "ignorance-fuelled hostility to religion, widespread among secular liberal elites" is a great "danger". In relation to music, it actively seeks to cover the fact that many of the best composers of the recent past – from Stravinsky, through Arvo Pärt and John Cage, to Taverner – have explicitly drawn on their religious commitments. That commitment is vital not incidental, MacMillan continued. It provides the soil into which the composer can sink roots from which to draw nourishment.

The implication is that by ignoring these wellsprings, music itself is impoverished. MacMillan referred to the music industry as a manifestation of that paucity, the notion that music is not primarily for and about human flourishing and wellbeing but is for and about the generation of a profit. "Extraordinary how potent cheap music is," quipped Noël Coward. MacMillan's complaint is more serious: it leaves people incapable of the "active listening" required to appreciate musical depth, an activity that is not unlike meditation and prayer. That matters not a jot to the commercial enterprise of the music industry. The fear is that people are not freed by music but are lulled into conformity.

The question of the nature of music is an important one, and one that will no doubt continue to lead to mystery. In his recent book, Musicophilia, Oliver Sacks makes many interesting observations about music though is unable to draw firm conclusions. Aaron Copland arguably hit the nail on the head when he wrote:

The whole problem can be stated quite simply by asking, 'Is there a meaning to music?' My answer to that would be, 'Yes'. And 'Can you state in so many words what the meaning is?' My answer to that would be, 'No'.

However, MacMillan's contribution was muddied by the insidious climate in which he writes, namely that of heightened aggression between belief and non-belief. Hence his lecture turned from being a celebration into an attack. Putting the question of music itself to one side for the moment, that highlighted a wider difficulty that we need to be overcome.

For the lecture was spoilt by its combative nature. And that in turn was because its aggressive overtones perpetuated the discourse that the new atheists, and their religious mirror opposites, would have us pursue. It's a difficulty because it is hard to resist following the rules set by these bitter protagonists – rules such as whether you are for or against faith, whether you affirm or deny the existence of God, whether you believe spirituality is humanly enriching or a slippery slope to superstition. These days it is almost the case that you have to declare your interest, as it were, before you can proceed.

I think MacMillan wanted to appeal to a more open, more interesting middle ground. His conviction is that music is a bridge, not a divide, between belief and unbelief, and he wants a genuine pluralism to thrive. And yet by referring to an "ignorance-fuelled hostility to religion" that is "bland and naïve" he risks destroying the bridge by forcing his listeners to take sides. Taking sides too soon is what is culturally and humanly damaging.

So how can the narrow discourse be sidelined and a richer one be pursued? There are individuals of no particular persuasion asking similar questions about music and art. They offer a way forward beyond the quick divides. Take critic Matthew Collings. In his TV programme, This Is Civilisation, he charted how the art of the past and present alike is founded on a religious impulse, though the latter period might often deny it. Even humanistic art since the 18th century invokes the aura explicit in earlier religious art; it quotes from religious art to gain authority.

But then Collings poses the key question: what happens when you remove the divine from the philosophical equation: "Once the religious structure of life is removed, even if temporarily, what is there for art to do?" It can enter the business of expressing human feeling. Or, in the world of music, it can become "absolute music", a music that doesn't refer to anything beyond itself.

However, Collings for one does not underestimate the crisis precipitated by what Nietzsche famously called the "death of God", the crisis that similarly causes MacMillan such concerns. For Collings, it is this crisis that has led so much contemporary art to become merely gleeful, giddy and weakly menacing. For MacMillan, it leads to the "soul destroying" tendencies of the music industry.

Nietzsche himself thought the crisis would last for centuries. There is no ready resolution to hand. But both MacMillan and Collings are pointing us to the crux of the matter. We must follow their lead and resist the fundamentalists and their despisers.