Last week we were treated to the sight of hundreds of British doctors voting on whether homeopathy has a place in the NHS – a surreal spectacle on a par with watching a geologists' union arguing what their position on the likelihood of a flat Earth should be. Naturally BMA members voted overwhelmingly in favour of the motion that homeopathy should not be provided on the NHS, but many among their ranks were sceptical of the move, and not all of them were believers in 18th century magic.

In fact their arguments weren't really about homeopathy at all, but made a compelling case for a wider debate about British medicine's elephant in the room – the placebo. I talked to one of those who spoke at the BMA debate, Dr John Garner. "Though we are all in favour of evidence-based medicine, all GPs know that there are patients who don't have evidence-based symptoms," said Dr Garner. "These patients after full investigation do not respond to conventional medicine and some find benefit in homeopathic treatments."

Garner made three points to me: that we shouldn't be withdrawing treatments that work for patients (whether this is a placebo effect or not); that the medicines these patients might otherwise be given, such as painkillers, SSRI antidepressants or antibiotics, may have side effects or be more expensive; and that by catering to their whims "we keep the patients in contact with conventional medicine so if their symptoms change they are not alienated from mainstream medicine".

Before we continue, let's be clear, an argument for placebos is in no way an argument for homeopathy. For one thing, homeopathy is a rip-off – why should the NHS pay a fiver a time for magic sugar pills when a tube of Smarties costs 50p, comes in lots of different colours and has pretty much the same evidence base?

And as happy as many people are to believe that medical training can be replaced by Google and a DVD box set of House MD, the fact is that homeopaths are not trained in the same way that doctors are to make diagnoses or give out prescriptions. Nobody claims that all real doctors are perfect either, but with the best will in the world, giving homeopaths responsibility for front-line medicine is like letting toddlers fix your car because they can drive a go-kart and make "vroom vroom" noises.

But the inconvenient truth for me, the BMA and for sceptics who backed the recent 10:23 campaign against homeopathy is that those who opposed the motion actually have a bit of a point. A fact nobody disputes is that for some patients, homeopathy works, just as any sugar pill would. Is there therefore a case for allowing placebos – and by extension alternative medicine – to be used in treating patients?

The science and technology select committee's "evidence check" on homeopathy earlier this year specifically tackled the issue of placebos and gave them short shrift. In its written conclusions, it quoted the comment from NHS West Kent's medical director Dr James Thallon that, "When doctors prescribe placebos, they risk damaging the trust that exists between them and their patients."

But the committee's discussion of placebos focused on ethics rather than pragmatism, and in the real world the ethics may not be as clearcut.

When questioned by Liberal Democrat MP Evan Harris during the evidence check, the then minister for health Mike O'Brien highlighted this dilemma: "I would not be happy to be misled and I suspect most patients would not. However, that was not the question you asked me. What you were asking me ... was whether it would be unethical for a doctor ever to prescribe a placebo ... I thought about it and I took the view that there might be circumstances, but would you generally do it? Of course you would not."

Dr Ben Goldacre took a similarly nuanced view at the hearing, with an argument that echoes Dr Garner's: "There are often situations where an individual may want treatment, for example, but where medicine has little to offer – lots of back pain, stress at work, medically unexplained fatigue, and most common colds, to give just a few examples. Going through a 'theatre' of medical treatment, and trying every medication in the book, will only risk side-effects. A harmless sugar pill in these circumstances may seem to be the sensible option."

Mention placebos to the General Medical Council, the doctors' disciplinary body, and the response is somewhat muted. Several times in the past year, I and others have asked the GMC to clarify its stance on both homeopathy and the placebo effect, and in each case I've been referred back to the same guidance, which reads as follows, but could be interpreted in many ways depending on your definition of "benefits":

"We do not require doctors to use only evidence-based treatments, in any form of medical care, but we do expect doctors to do their best to ensure that any treatment they offer is in the patient's best interests. This will generally mean that any known risks of the treatment are outweighed by the potential benefits to the patient."

There are no easy answers here, and with existing guidance as vague as this doctors are left to make their own judgement calls about the use of placebos.

I believe homeopathy should be consigned to the history books, so I'm happy to see doctors standing up to ignorance and calling for a ban. But a bigger debate should be had about the role of placebos in healthcare, because at the moment they're being used anyway, and simply banning them one by one on an ad hoc basis probably doesn't constitute an effective health policy.

Martin Robbins writes for The Lay Scientist