Am afraid to say that most likely you would need a new sunroof, Me and my friend had the same problem in our X5's and both needed a new sunroof. His car was on warranty so he got his done for free, my car was 1yr out of warranty but i was able to get a discount of £800 for the part (normally £1800) but had to pay £650 labour.

Is your car out of warranty? if so i would call BMW and see if you can get a goodwill gesture to reduce the price a bit.