They have tested for all the bacteria and viral issues that are common, giardia, rotavirus, all of that good stuff. Colonoscopy would not help since they would have to go to far in to do anything and you can't do a biopsy on a squirming child.
Like Ttrina said, food allergy test would take 10 minutes to draw the blood, and the results back in a week.
Taking music moms analogy, its more like ordering an operating room to set the broken bone before taking an x-ray.
The only reason the doc came up with for doing the biopsy is to check to make sure it is not celiac, if that is the only reason she has, then we will put her on a gluten free diet before allowing them to put my child under anesthsia!!