This seems to be two different problems. The pediatrician saying that your baby is using you as a pacifier doesn't necessarily mean that her having a pacifier is bad.
Generally speaking, it's still thought to be best, breastfeeding-wise, for a baby to not be given a bottle or pacifier until they're sucking at mother's breast like a champion. Your daughter apparently got that far, so given that, a pacifier shouldn't be a problem.
What the pediatrician may have been alluding to is that your daughter, at only a few weeks old, may be getting all she needs from you food-wise in a relatively short window, and after that is dropping down to a lighter, shallower "non-nutritive sucking" pattern, the same as she'd use with a passy. The difference between this pattern and the pattern she'll use when she's really interested in food is very different; nutritive sucking is hard, long, and she'll be regularly swallowing and gasping (which is why you have to burp).
At that point when she starts to drop down to non-nutritive suckling, the value of keeping her at the breast is diminished; she's there for comfort, not food, and so you can take her away from the breast, give her a passy, and do something else with your time. An hour to an hour and a half at a sitting, when a newborn typically should be fed once every two hours, theoretically would mean you spend at least half your time nursing, and that's not healthy for you.
If you have a pump, try pumping, and see how long it takes from the moment you turn the pump on to get 2 ounces, or however much the baby books say your child should be eating at her age. My guess is that it will take closer to 15 minutes than to an hour and a half. However, there's no strict time limit here; if she's still sucking hard at the 15-minute mark, then let her keep going. She's a growing girl. Depending on what she weighed at birth, she's likely to quadruple her body weight in the first year, and all that energy and all those protein building blocks are going to come from you, God willing.
I would bring all these concerns to a breastfeeding coach. The hospital our daughter was born at had a breastfeeding clinic literally right across the entry bay from the maternity ward. It was staffed with nurse practitioners who did nothing but counsel new moms on how to breastfeed. I would see if there is any facility like that in your general area; these guys know breastfeeding, regardless of the experience your pediatrician has on the subject.