L.,
You are certainly not alone in this delimma!
Our son had the same issue through age 4. He was on a prescription for almost a year, after that we gave him one Fiber 1 tablet a day. It was an easy way to get enough fiber into his diet and he liked the flavor of the orange tablets.
Like you I did not like to give him the perscription, I don't think that any parent wants to shovel medicine into their childd. But also, being in the medical profession myself, I understood the risks that go along with withholding. The benifits of helping his system get on the right track and then maintaining it with a healthy fiber supplement, far outweighed my own personal hang up with giving him the meds.
By the way, he is 5 1/2 now and we have not had any problems in over a year! He does not even take the Fiber supplements any more. The only thing that we are careful about it making sure that he gets lots of fruit in his diet - which we should do anyway!
Good luck!