I think you can email Etsy and explain the situation and they can remove the negative comment. You refunded her the shipping costs and you had no control over shipping. I think you did everything you could and the negative feedback was uncalled for.
I had a shipping mishap too. Someone sent me a message about getting something before Christmas, I charged her extra for priority mail. Somehow the man at the USPS store typed the info in wrong, it was suppose to go to Maine, but was programed to go somewhere in CA. The Friday night before Christmas, after the post office closed was when she contacted me to let me know it wasnt there yet, so I couldn't do anything about it until Christmas Eve. Luckily she is also a shop owner and was very understanding about the post office mishap.