I think you are doing the right thing by leaving the medications. The medicine like others has said decreases the acid, but doing this is stops the burning feeling in the osophegous, and this is what causes the pain.

But if she isn't crying and gaining well, then it is best to leave it. The medicine will not stop the vomiting, as this is caused because of a weak or immature lower osophegeal sphincter and the medicine doesn't strengthen that so stuff will come up still. But keep an eye on her weight and feeding and if you notice a difference, then you can always talk to your doctor about it.