I wouldn't worry about it. It's a very minimal amount of radiation. The things they were looking for would have required surgery, and fairly soon, so it was better that they rule them out sooner rather than later. I'm sorry he had to have the test, and I'm glad it came out okay. I, too, was hesitant when my baby girl needed testing, but come to find out, she had a very difficult to manage condition that leads to lifelong procedures, such as esophagus stretching every few months due to scarring, if left untreated. Did I want the tests? No. Am I glad we can hopefully prevent a lot of future pain and anesthesia for her? Yes! Yes! Yes! If you just can't get your mind to rest, go back to the doctor, and share your concern. The doctor should be able to explain why the prodedure was recommended, and what they were concerned about that out-weighed the risks. If not, find a new doc. Anyway, I'm glad it turned out well for you.
PS -- My 9yo son had one done at about 2 or 3 months old, too, to rule out Pyloric Stenosis. Thankfully he didn't have it. So far, he has no problems from the testing.