Your GP is totally ignorant - I would not trust him - I would want to be referred to someone who knows about CD, or at least to try a different GP at the practice. Young ones are often better informed than old ones, though even young ones are often woefully ignorant.
On children that young, the blood test is often unreliable because their immune systems aren't fully developed so they may not be producing enough antibodies to register in the blood test. If I were you, I would ask to have the genetic test that shows whether or not they have the DQ2 or DQ8 'coeliac genes'. Having the gene doesn't mean that you are coeliac as there is also an environmental trigger involved, but NOT having it means that you're not. About 33% of the UK population have the gene.
I will be having DC3 tested for the gene next year when she's 3. Both her siblings are coeliac, and as a family we are now gluten-free. If she doesn't have the gene, then I know we don't need to worry about her. If she does, then we will do a gluten challenge when she's older and test for it.
Ring Coeliac UK and ask for help, they can advise on diagnosis. You certainly need to be eating gluten, and a considerable amount of it, every day for at least 6 weeks before the test.
The blood test looks for antibodies in your blood that coeliacs make in response to gluten in their digestive system. No gluten, no antibodies. If you've been gluten-free for a long time, it takes a while of eating gluten for the antibodies to be produced again.
The endoscopy looks for damage in your villi caused by the antibodies attacking your small intestine. Again, no gluten, no damage. The villi heal gradually once you go gluten-free.
The first inkling we got of my then 3yr old's coeliac disease was that he was anaemic. It improved on iron supplements but went down again when he came off them. Stupid paediatrician decided it was our fault for not feeding him enough iron-containing food. Took a year and a half before we got an intelligent paediatrician who noticed his hard, bloated belly and asked us about his bowel movements, then sent us for a test - sky-high, off the scale antibodies. A year and a half later, he is so vastly better it's unbelievable.
Are their poos yellow and frothy/floaty? Look up 'steatohrrea' (sp?!) to see a description. That's quite a strong indicator. It makes me concerned about DC3, because when I've tried putting her back on gluten, she has these kind of poos - hence testing her for the gene next year.