Well first off, even if only for a short period of time, any breast milk you have provided for your daughter has given her a great gift. Don't feel guilty or otherwise.
My daughter has a milk allergy, which our pediatrician said is possible for her to outgrow. And she too is breastfed exclusively. Clearing her system of milk took about a week and half after we eliminated the entire dairy in her diet (mine as well). After that we switched her regular formula supplement with Hypo-allergenic formula. It is more expensive, but will solve any of the discomforts she's having. Our pediatrician said that soy might work, if only for a while. (Some babies with milk protein allergies can become allergic to soy protein after awhile as well.)After a week or two she decided that she didn't want a bottle or formula any more, which ultimately saved us money :p
In the end, I couldn't bear to give up my breastfeeding bond with my little sweetheart. Although it was dreadfully difficult to give up dairy for so long, it has been worth it. She's developing so much it amazes me, and makes me happy to know I've contributed a great deal to that. I haven't had any dairy for 4 months now, and after the 2nd month is was easier. If it provides any comfort, we tested some dairy in my diet the other day and so far she hasn't had a reaction. It is possible for them to outgrow it in as little as 4 months; though every case is different.
In the end it is your call. Good luck and hope your little one feels relief soon!