I think the next step would be that when you add a product to the registry there's a checkbox like "let people buy this from other stores" which is default checked on amazon/babys-r-us and default unchecked on etsy.com. Then in the registry display you would see multiple offers for one product. Then there would still be the challenge you describe but it wouldn't be a UI problem, it would be a data challenge.
Our site, which was on HN a few days back actually does the price comparison shopping, as well as integrating with traditional registries. There was a lot that went in under the cover of how to import and push a registry to a traditional registry, but allows us a complete solution of showing guests the best price. (http://www.registrystop.com) We're more targeted towards wedding, but would love to do the same for baby registries.
I think the next step would be that when you add a product to the registry there's a checkbox like "let people buy this from other stores" which is default checked on amazon/babys-r-us and default unchecked on etsy.com. Then in the registry display you would see multiple offers for one product. Then there would still be the challenge you describe but it wouldn't be a UI problem, it would be a data challenge.