Most GPs I have seen, both in the UK and Australia, are pretty good - but there are a few that really aren't. IME, the ones who aren't, are the ones who are convinced of their own rectitude and really fail to listen to the patient properly.
Bad experiences:
• my brother could have died from peritonitis. His GP failed to diagnose acute appendicitis, because the pain "was in the wrong place". By the time he was admitted to hospital, he had a tennis-ball size ball of pus around his appendix, which had to be drained before he could be operated on - if that had burst, my brother could seriously have died. He was on IV antibiotics as well and was in hospital for nearly 3 weeks.
• My niece - at 16mo was running happily around. By 18mo was falling over A Lot. By 20mo could no longer walk. She had had various episodes of sudden sickness (vomiting), lassitude, and then started fitting. The GP (and, to be fair, the hospital) put it all down to, variously, ear infections, teething, tonsilitis, febrile convulsions (despite her not having a temperature).
She had a brain tumour in her cerebellum that was blocking the ventricles, her CSF was under enormous pressure in her head. Eventually, at 21mo, my sister took her to KCH in London, where they did the necessary scan and found the walnut sized tumour. She was kept in, had a shunt put in the next day (10 foot jet of fluid across the theatre, apparently) and 2 days later had the 9h op to remove the tumour.
I know brain tumours in children that young are rare. I know that it's unlikely that the GP would have seen one before, and possibly even the local hospital - but they also wrote my sister off as neurotic, too anxious etc.
My niece could also have died, because of the increasing pressure in her brain, as the tumour grew. Luckily she didn't, and is still with us.
• The Gp who told me, 2 weeks after my first MC, that I was "too old to have another baby, should just be grateful I have one and stop trying". He is also a head of practice, and the only GP who always has appts available.
• The Gp who wouldn't listen to my problems with my own balance, just told me I was too young for degenerative arthritis in the neck and to get on with it.
Good experiences:
• the GP who came out to see my mum, and against mum's wishes, sent her to hospital - she had a burst diverticulum, also had peritonitis and would have died within the next 3 days if untreated. She needed an emergency colostomy and lasted another 10y (finally dying of bowel cancer).
• my Dad's GP - who listens and has sorted Dad out several times wrt DVTs, kidney stones, prostate cancer etc. etc.
• my own GP - sent me for physio for my neck and migraine problems, also referred me to ENT re. my balance issues (they got it completely wrong at ENT, but never mind - osteopath fixed my neck in 2 treatments and the vertigo went) and also listened.
But going back to the OP (sorry for the me-rail!) YANBU to think that the GP should not have gone against the consultant; if they didn't want to take the prescription risk, then they should have told you to go back to the consultant for the prescription, not given you the bollox they did. And as for saying your DD could go back onto cows' milk - gahhhh!