Be very careful with Depo. It is proven to pull calcium from your bones.
I have tried Depo before, I gained about 20lbs on it. I had a spotting daily for MONTHS! I couldn't handle it. After I had my son, I got the Mirena IUD placed. I absoultly LOVE it!! I did have some spotting for the first month, but then my periods basically disapeared. I haven't gained any weight on it, and it's good for 5 years. Obviously the decision is yours, but with your malabsorption, I wouldn't risk the calcium loss of the Depo.