My son often has green stool too. Even though it is quite alarming to see, his pediatric gastroenterologist was not concerned at all. My son has a history of stomach aches, extremely large bowel movements, vomiting, bloating and excessive gas, which can be lethal! He has been diagnosed with reflux (a disorder where, basically, a "flap" or "door" between the esophagus and the stomach doesn't open and close properly, which causes stomach acid to rise up into the esophagus. It is very common. The treatment is prescription Pepcid and/or Propolsid.) He also has some food allergies (milk, eggs, tomatoe sauce). In any case, I've expressed my concern about the discoloration several times and the doctor (a specialist) always reassures me to not worry about it. Just thought I'd let you know.
My 6 yr old son used to do the same thing when he was about 3, but his were frequent. If it continues and he complains of stomach upsets and also has frequent vommiting after eating, have him checked for a Candidia yeast overgrowth. That was my son's problem. Lots of sugar in the diet, lots of dairy products, frequent antibiotics (for strep, ear infections, etc.) can cause the bacteria in the "gut" to get out of whack. Acidophilus/bifidus tablets are good for this, as is caprylic acid tablets.
But if the green stool is not recurring then I wouldn't worry.
I think the doctor is giving you sound advice. If there's a repeat of the experience, the doctor could have a stool culture done, but this probably won't be necessary.