He wrongly accused a mother of killing her son. But should a leading paediatrician have been struck off? Jeremy Laurance argues that vilification will only make it harder to expose abuse

One outcome of last week's decision by the General Medical Council to strike Professor David Southall off the medical register is certain. Children living in abusive families will now be at greater risk.

What is harder to assess is who is responsible for this outcome: Professor Southall with his crusading zeal; or the GMC, desperate to shake off its image as a cosy club protecting doctors? Professor Southall was found guilty of serious professional misconduct for accusing a mother of drugging and murdering her 10-year-old son. The boy was found hanging from a curtain rail at his home in 1996.

Professor Southall had been appointed by the Family Court as an expert witness to give his opinion on what had happened and to help them assess the vulnerability of a second child in the same household. The events took place nine years ago and the interview with the mother, identified as Mrs M, was conducted in the presence of a senior social worker. Professor Southall denied the woman's claim that he had accused her of murder, insisting that he had raised it as one possible scenario to explain her son's death.

His account was backed by the social worker, who gave evidence to the GMC over two days based on handwritten notes made at the time. But the GMC chose to believe the evidence of the mother, dismissing the social worker's account.

This has, unsurprisingly, alarmed other paediatricians working in child protection, who feel a key part of their defence against false accusations the presence of an independent professional witness has been demolished by the decision. Thirty-nine of them wrote a joint letter to the press setting out their anxieties about what many describe as a "perverse" decision.

Patricia Hamilton, president of the Royal College of Paediatrics, warned in a statement immediately after the verdict: "We are very concerned that paediatricians and social workers will be deterred from undertaking child protection work and that children and young people will come to harm."

Behind this coded message lies growing concern about what paediatricians say is a witch-hunt against them orchestrated by a small group of affected parents, aided by certain parts of the media. They refer to the "concerted campaign to deny the reality of child abuse" and point to the fact that while cases on the child abuse register fell by 28 per cent between 1995 and 2005 (so fewer children had protection), criminal convictions for abuse and neglect rose by 245 per cent (from 1998 to 2005).

A second plank of the GMC's decision referred to Professor Southall's habit of keeping separate files on child abuse cases he was found guilty of doing so in seven instances. This, according to Cassandra Jardine, writing in the Daily Telegraph, was an even more heinous crime: "A doctor who removes or destroys records cannot by any stretch of the imagination be said to be acting in the best interests of the child."

Yet, the keeping of separate medico-legal notes, although not sanctioned, is widespread for the obvious reason that it is difficult to record sensitive information in a file to which the parents have access. Again, paediatric colleagues consider the GMC's verdict perverse. The chief requirement is that the records are clearly signposted so that professionals can locate one set from the other. The failure to do so was a key reason why Victoria Climbie, who suffered months of abuse before she was killed by her carers, slipped through the net.

A third black mark against Professor Southall was that he had form. Three years ago he was found guilty of serious professional misconduct after he accused the husband of solicitor Sally Clark of murdering their children. He had seen Stephen Clark give a TV interview in which he said his two-month-old son, Christopher, had developed a nosebleed while in bed in a hotel room. Based on his experience of child abuse, Professor Southall believed that spontaneous nosebleeds were rare and often associated with trauma, such as that caused by attempted suffocation, and raised his concerns with the police.

In the new case, the GMC cited his failure to apologise for this episode, which lent support to their overall conclusion that he had "a deep-seated attitudinal problem". But he has made clear in interviews since 2004 that he still believes he was right to raise concerns about Stephen Clark, and he was backed by 53 UK paediatricians in a paper in the American journal Pediatrics, which argued that the GMC's 2004 verdict "conflicted with child protection laws and guidance for professionals".

However, the GMC's diagnosis of an attitudinal problem goes to the heart of the case. Every profession needs its pioneers, those who are prepared to test the boundaries and advance medicine. In the field of child protection, Professor Southall was that man, doing groundbreaking work in the 1980s and 1990s in developing the technique of covert video surveillance that secured the conviction of dozens of abusive parents.

But his critics say he did not merely test the boundaries but crossed them, in his overzealous belief that children must be protected at all costs. A senior paediatrician and expert in child protection said: "It is a matter of personality. Other people would have approached the interview [with the mother, Mrs M] differently. You are dealing with disturbed, distressed and anxious people and it is about communication how do you tackle a very difficult conversation and come out of it without making them feel worse?"

It appears to be Professor Southall's personality, combined with his "lack of insight into the multiplicity" of his failings, that most alarmed the members of the GMC's Fitness to Practise panel. They found him guilty of serious professional misconduct and could have issued him with a reprimand or suspension (he is already suspended from work in child protection, since the 2004 case). Instead, they struck him off, eschewing the lesser sentences. Even those who think the verdict right were shocked by the severity of the punishment, which has been widely criticised as disproportionate.

The GMC has a duty to protect patients but as Professor Southall is already banned from child protection work it is difficult to see how this is an issue. He is now considering an appeal and the GMC says it cannot comment pending that possibility. But whatever the outcome, the febrile atmosphere generated around child protection means children are already the losers in this unhappy case.