Hi there,
Thanks for your query.
I agree with you regarding the possibility of 
gluten allergy, because of which you are suffering from 
malabsorption syndrome.
Your Vit D level is really low. But, taking Vit D WITHOUT 
Calcium supplement, will be futile. You should ideally take 
Calcitriol (Vit D3) 0.5-1.0 micrograms / day, along with at least 1000mg/day of 
Calcium carbonate.
Further, osteopenia denotes protein deficiency. hence, you should have a high protein diet. 
I would suggest that you get 
*     Blood Parathormone levels estimation done to rule out/detect hyperparathyroidism
*     Kidney function tests to rule out/detect underlying kidneys problem. 
Consult your doctor and apprise him of my opinion. I am certain that he will agree with me, order required tests, and- based on the reports-  will prescribe suitable/modified treatment as advised.
If you find my response helpful and informative, do not forget an “excellent” (5-star rating)  to my answer, to ENCOURAGE ALL doctors- engaged in social service- to render sound advice to the FREE queries. 
Take care
Dr. Rakesh Karanwal