I buy on eBay routinely and have had only a couple of damaged items but many that were poorly packed. It's a wonder the items weren't damaged! I've done what you did...contact the seller about the problem. If they offered to make it right (refund, adjustment, anything) then I gave them positive feedback even if I declined their offer. As long as a seller makes the effort to try to fix the problem, regardless of whose fault it is, I feel that they lived up to their obligation as a seller.
But if they don't make any kind of offer of adjustment and/or try to blame their inadequate packing on the shipper, then I would leave neutral and state in the comments that the item was as represented, etc., but shipping was a problem. Every seller knows that shippers are rough on packages, it's the nature of the business, and they should pack carefully enough to allow for the nature of the shipping business.
Anita