Can a Polar Bear Fence be Allowed Clearance?

I think your best approach here would be to decide what a reasonable offset is for this fence and propose that to USGBC when you submit the credit for review. It's such a unique project requirement, that your team almost certainly has more expertise than the LEED reviewer on how much area you need to disturb and what you can do to prevent habitat damage. If you put togehter a narrative and diagram showing the dimensions of the pilings and the limits of disturbance and the measures you are taking to keep the disturbed area as small as possible, I bet that will be acceptable.