If you are happy you have tried everything then there is no reason to feel bad about medicating her - the meds exist for a reason and if they don't help her then you can always stop them again.
Yep, sometimes medications are needed. You can try to control diabetes with diet and lifestyle, but sometimes meds are needed. Same with asthma and a heap of other conditions. Maybe the same for your little one's condition. Hope you can become comfortable with your decision.