Rebif isnt a treatment for Lyme disease or gluten sensitivity.
I have to assume that because you're not sure what is causing her MS, she is in 'just in case' mode.
Although, if she hasnt had a relapse in the 4 years she has been using Rebif then couldnt you pretty much rule out Lyme and/or diet as being the cause?
Has she had any relapses or exacerbations since starting Rebif?