Well, I don't think your doctor recommended the change in eating habits because he/she thought anything was "wrong," it was probably suggested as a way to help you feel better. If you go in to your doctor's office complaining about bloating and general stomach discomfort, they're going to try and help. If they truly thought something was wrong, they're order tests.
You can take their advice or not—keep eating three big meals or have six smaller ones—the choice is up to you. There's no guarantee that eating six small meals a day will make anything better, it's just the least invasive thing your doctor could think of to suggest for symptom alleviation. Remember, they're making suggestions because you sought their advice! So often we hypos run to the doctor when we think something is wrong, but if they say anything that might suggest they too think something's wrong, we freak out. That's very contradictory thinking. When it comes to doctors visits, we can't not expect to get what we ask for.
Challenge your own thinking in this matter. Ask yourself if your feelings of resistance have a logical basis—is it realistic to be fearful of making these dietary changes? I realize that's easier said than done for us anxious types, who tend to run on emotion, but it's at least worth a try.