A.,
When my son was a baby, he had colic, and all sorts of problems with his bowels, due to the iron in his formula. The only way I could get him to have a bowel movement was to use a glycerin suppository every day. I did this right up until he began eating fruits and vegetables, along with his cereal, which finally straightened out his bowels, so he could go on his own.
If I used them on my son every day, at that age, I seriously doubt if using one occasionally with your son will be that big a deal....my son is now 29 and is 6 feet tall, and it didn't hurt him a bit! Sometimes I think these pediatricians just like to be alarmists about using any sort of laxative. However they do work.
Another thing you can try, if he isn't moving his bowels, is to put a teaspoonful of liquid Phillips Milk of Magnesia in his bedtime bottle. Its very gentle, and he will probably have a bowel movement for you the following morning. Your pediatrician probably won't want you to do that either, but again, it does work.
My grandmother, who raised 5 kids, told me to do both of these things, and they both worked great, and made my son much more comfortable. She said that today's pediatricans are very knowledgeable, but sometimes the old ways work just as well, and she was right!
Give either of them a try, and I'm sure your son will go regularly, and be much more comfortable!