I have been there too! It is distressing when they are feeling poorly and you aren't sure how serious it may be.
The fact that there is no fever, nausea, vomiting, and that the pain is intermittent are all good signs. You did the right thing to call the Dr. Could just be a pulled muscle or something fairly benign. Is it in an area that has caused pain before? Does is seem worse right after a meal? Is he feeling full more quickly after he eats? These clues can give you an idea if the pain is intestinally related, or muscle related.
In our experience, even when my son was headed towards solid remission, there were times he had pain. Whether is was gas, crohns, infection, I am not sure but it always seemed to pass. I have learned now that there are ups and downs and have been better able to understand what is normal for him and what seems to be a sign of trouble. If it were my son I wouldn't be worried but I would do as you are doing and check in with the dr. The Dr. will probably give it some time to see if it gets worse or better. I find that most things with this disease are a 'wait and see'.
Keeping my fingers crossed the pain goes away and no surgery needed!! Let us know what the Dr. says and how your son is feeling.