oh my god Shelli DO NOT GIVE YOUR BABY A SUPPOSITORY! SHE IS FINE! thank god you are breastfeeding, that is SO wonderful. but you need to know that pediatricians are very hostile, even if they pretend not to be, toward breastfeeding mothers. so don't go on your doctor's advice. your baby is NOT sick.
first of all the best information on all this is at the La Leche League Int. website; go there and find your local chapter; go to a meeting to discuss this concern if you can, or contact your local chapter leaders. what you're experienceing is totally normal and totally fine.
breastmilk is extremely efficient; exclusive and near exclusive breastmilk fed babies will very often not poop because there's nothing leftover to get rid of! :) breastmilk is nature's single perfect food. so your baby is just using up all her food, and not to worry.
my children have never had formula but they both started food early, at about 5 months; but much more of the food got ON them than IN them. once they did start eating food they started pooping a lot. but prior to that they often didn't poop. before i knew anything about breastfeeding, i had the same experience as you and was worried like you; i gave my son about 2 teaspoons of raisin juice which i made by boiling and straining raisins. it did not work! so don't worry about the prune juice. you can keep giving it to your baby in small quantities, like a teaspoon at a time, but don't expect it to do much. it's not poison, it's just food, and that's perfectly fine.
LLLI asserts that babies should not have any solid (or soft incl.) food of any kind before 6 months, and that's fine; i didn't do that, obviously, but there's no reason NOT to follow that rule. but a little prune juice is not a problem.
what IS a problem is a suppository; giving medicine to any person who isn't sick is extremely risky, and i really hope you will not do this. if your baby was showing any signs of being sick, that would be different. i am glad that you see the difference. you're obviously a very tuned-in mom. i would really wait until the baby seemed uncomfortable or unhappy before going back to the doctor. remember that doctors stay in business and stay important because they have "answers"; but they often create answers where there don't need to be any. i would say stick with your obviously excellent intuition for now.
i would also say to you, why use formula at all? you could just pump a bit more, if you need to, or offer your baby the actual breast a few more times per day. breast milk is really so very much better than any formula; anyone who says otherwise is less informed than they should be. you're doing a great job, why not fill in that one or two feedings? your body will naturally make more if your demand goes up, i promise you won't run out.
good luck to you! your baby will be fine!