In the early 1970s, at a school near Pontypridd, two teenagers sat in a physics lesson and discussed whose was the best dad. Until then, Gethin Russell-Jones had counted the other boy, Mark, as a friend – but not this day. “Mark said that his dad’s job as a fireman was useful whereas my dad, a Baptist minister, probably did nothing from one Sunday to another.”

The conversation turned to war. “At that time, the question of what people did in the war kept coming up,” says Gethin. Mark’s dad had fought in North Africa during the second world war and Gethin recalls reddening as he told Mark that his dad had been a conscientious objector. He had had to explain what it meant as Mark didn’t know the term. He was incredulous. (“What sort of man did that? Did he agree with Hitler? Didn’t he care?”)

Gethin rushed to his father’s defence (ironically, a full-on fight followed). But that schoolboy exchange plagued him for decades because, more and more, he found himself agreeing with Mark. “When I was very young, six or seven, I remember feeling quite proud that my dad had been a conchie – that he’d said no,” says Gethin. “It made him different, gave him a mystique. As I got older and learned more about the war, it became more of an issue. At some point, I began asking Dad what would have happened if the Germans had invaded. He had no satisfactory answer.”

Last year – by then a Baptist pastor himself, as well as the father of four adult children – Gethin began to delve deeper into John’s story. His book Conchie: What My Father Didn’t Do in the War is the result.

Ironically, the project had its origins in a book Gethin had co-written two years earlier with his mother, Mair, about her own war experience.

In the face of something as monstrous as Hitler, or Isis, what do you do? You can’t do nothing

In 1940, Mair had been studying music and German at Cardiff University when she was recruited by the Foreign Office (there really was a tap on the shoulder from a man in a dark suit) to join the code breakers of Bletchley Park. Bound by the Official Secrets Act, Mair remained silent on the subject until the final decade of her life. She died, aged 96, on the day My Secret Life in Hut Six was finished.

“My father died before Mum – and it was almost a challenge to see if I could write about him and what that would look like,” says Gethin. “My mum was positive, pragmatic, resilient – she had this huge narrative of the way she dealt with Hitler. My dad had an ideology, but what was his story?

“My mum had always been more accessible. If I needed to talk about something, I’d instinctively go to her. Dad was more aloof, always a bit removed. There was an isolation about him. He was cloistered, quite monastic, uncomfortable in wider society. Being in a pub, for example, or at a rugby match, was just awkward. In a way, this book is the typical story of a son struggling to understand his father.”

Conchie draws extensively on John Russell-Jones’s journals, memoirs and sermon notes, which had been packed away for decades in a draughty garage. “I’m the youngest of five but none of us had really looked through them,” says Gethin. “From time to time, we’d think, we really should transcribe these.’ Much of it was scribblings, some in battered old diaries, some on the back of old electricity bills. None of it was linear. I had to get used to finding random gems.”

Pieced together, they create a vivid picture of a boy coming of age in the aftermath of the first world war and the shadow of Hitler’s rise to power. Born in 1918, John had a Welsh working class background – his father and grandfather had been tin plate workers and John was the first in his family to go to grammar school and university.

John describes one of his teachers, a brilliant Oxford scholar, who had returned from the Somme a “nervous wreck”. That war was supposed to have been the “war to end all wars”, yet already unease was creeping across Europe.

For John, family life revolved around the chapel, where the minister was an outspoken pacifist. Inspired by him, 13-year-old John took part in school debates and gave speeches at a local literary society, arguing that warfare was incompatible with Christianity, that Christians should “work for justice and equality” and “against state-sponsored greed, including war”.

By 1939, when the National Service Act required men between 18 and 41 to register, John was studying to be a Baptist minister. Although this was one of the automatically exempt professions, he insisted on attending a tribunal to voice his protest and be officially registered as a conscientious objector. His careful preparations, his speech and the reaction of the officials on the board (one pointed out that the Old Testament was full of wars) makes fascinating reading.

It’s one thing to have convictions but to do nothing, to risk so many other people’s lives … it doesn’t seem right

From this point on though, the war seems to take a back seat in John’s life: he joins other Christian groups, he meets Mair (and notes that they “agree to disagree” on the subject of war). He glides seamlessly towards his calling as an ordained minister. Meanwhile, Europe is in turmoil.

“Going through his papers and looking at the timeline, I got quite irritated with him,” says Gethin. “Dad went from having quite a positive view, a belief that by getting together, we could make the world better, to a much narrower outlook, which was all about his personal faith. I don’t remember any diary entries which even mention world events. It’s 1944 and hellish in Europe and Dad’s disappearing down a rabbit hole of self-examination. I read them thinking, come on, Dad!”

For the rest of John’s long life – he lived until he was 92 – he barely spoke publicly about his pacifism, despite having a weekly platform on which to do it. It had morphed from a public protest to a private decision. “His whole life revolved around the New Testament. The Sermon on the Mount was his starting point,” says Gethin. “If you have an enemy, you don’t kill them. You forgive them, however hard that is.”

Despite sharing his father’s faith, Gethin remains torn on this point. “In the face of something as monstrous as Hitler, or Isis, what do you do? You can’t do nothing. It’s one thing to have convictions but to do nothing, to risk so many other people’s lives … it doesn’t seem right.

“When I researched the book, I spoke to family members older than me who remembered Dad at that time and a number said they just couldn’t imagine John going to war. They said, ‘He wasn’t a killing man. But most people aren’t killing types are they? There must have been millions of men recruited who were terrified, who’d never imagined picking up a gun. So that doesn’t really answer it.”

At the same time, Gethin can’t help but admire his father’s courage. “He chose to put his head above the parapet and he didn’t need to.”

He also envies his deep certainty. “To some extent, Dad didn’t really care whether he was understood or misunderstood,” says Gethin. “I’m more ambivalent. I duck and dive. For me, there’s a sliding scale of morality here. My dad was consistent. The pacifist he was as a 92-year-old man was the pacifist he was at 22 – ‘God loves his enemies. Jesus told us to love our enemies and turn the other cheek.’

“This was his view and nothing would shift that. You could say that’s intransigent and narrow – or you could say that’s quite a thing.”

• Conchie: What My Father Didn’t Do in the War by Gethin Russell-Jones is published by Lion Books, £9.99. To order a copy for £8.19, go to bookshop.theguardian.com or call 0330 333 6846