Richard Dawkins – author of The God Delusion and theorist of the selfish gene – could claim to be the most famous scientist in Briton. Lord Martin Rees – astronomer royal, former president of the Royal Society, master of Trinity College, Cambridge – is arguably the most distinguished.

Last year, Dawkins published an ugly outburst against the softly spoken astronomer, calling him a "compliant Quisling" because of his views on religion. And now, Rees has seemingly hit back. He has accepted the 2011 Templeton prize, awarded for making an exceptional contribution to investigating life's spiritual dimension. It is worth an incongruous $1m.

Dawkins is no stranger to pungent rhetoric when it comes to religion. But "Quisling" is strong even by his standards. It was originally hurled against fascist collaborators during the second world war. Rees, a collaborator? What was the crime that warranted such approbation? The Royal Society lent its prestige to the Templeton Foundation by hosting events sponsored by the fund, which supports a variety of projects investigating the science of wellbeing and faith.

Dawkins and Rees differ markedly on the tone with which the debate between science and religion should be conducted. Dawkins devotes his talents and resources to challenging, questioning and mocking faith. Rees, on the other hand, though an atheist, values the legacy sustained by the church and other faith traditions. He confesses a liking for choral evensong in the chapel of Trinity College. It seems a modest indulgence. The ethereal voices of rehearsing choristers can literally be heard from his front door. But for Dawkins this makes the man a "fervent believer in belief". And that is a foul betrayal of science.

I should declare an interest here, as I too would be what Dawkins calls an "accommodationist", (when he is being polite). I often write about the relationship between science and religion, and have been a Templeton-Cambridge Journalism Fellow, the beneficiary of a first-rate seminar programme organised by Cambridge academics, funded by the Templeton Foundation. But then I love the big questions.

Rees pursues them, too, through cosmology, a subject that clearly fascinates many for similar reasons. Is there life like ours on other planets? What is the nature of our connectedness with the stars? It is partly for his insights on such matters that he has won the prize. But if he is modest about what can be achieved for religious belief by science, he insists that scientists should not stray into theological territory that they don't understand.

Last year, when his fellow cosmologist, Stephen Hawking, declared in a new book that philosophy is dead, because physics is triumphant, Rees advised readers not to take too much notice. "I know Stephen Hawking well enough to know that he has read very little philosophy and even less theology," he said.

Other winners of the prize express similar intellectual caution, individuals including Paul Davies, John Barrow and John Polkinghorne. Interestingly, past winners display very different attitudes towards faith, too. If Rees is an atheist, Polkinghorne is a Christian and an Anglican priest. Davies is not, though he believes it is perfectly valid to pursue questions of meaning in the context of what is being discovered about the cosmos. After all, is it not remarkable that our universe has produced entities within it that ask such questions – namely ourselves?

But with Rees's acceptance, the substantial resources of the Templeton Foundation have, in effect, been welcomed at the heart of the British scientific establishment. That such a highly regarded figure has received its premier prize will make it that little bit harder for Dawkins to sustain respect amongst his peers for his crusade against religion.

When the cultural history of our times comes to be written, Templeton 2011 could be mentioned, at least in a footnote, as marking a turning point in the "God wars". The power of voices like that of Dawkins and Sam Harris – who will be on the British stage next week – may actually have peaked, and now be on the wane. Science could be said, in effect, to have rejected their advocacy. Rees brings a preferable attitude to the debate.