I've not heard that -- hell, I can't even get to the Sony ebook buying part of the new Borders web-site!
I wouldn't be surprised if it were to be true, except that it seems silly that they would carry inventory that you can't use in person anywhere. Get a plastic card which is attached to a cardboard baking and buy it at the checkout and then take it home and only be able to use it at the Sony website?
All the other giftcards that such stores sell can physically be taken into a store and used in person. It would be strange, but these days the retail world seems to be full of strange things!