I would leave feedback for the seller. As someone else mentioned, you can leave 'neutral' feedback - not positive or negative. That seems totally appropriate for this situation. The problems were not caused by the seller but he didn't take appropriate action to assure that the shipper could not cause damage.
If I was buying from this seller, I would want to know that he has not used proper packing on a previous sell before I bought something from them. I feel that feedback like that is useful for future purchasers and basically like a public service announcement for other eBay purchasers.