I did step up from a frys purchase of a 7900gs with the sole intention of doing step up after r600 came out and prices dropped. Well R600 was ALOT later than I hoped but I still got a relatively good deal on a 8800gts640. At the time I did it, the last day of my stepup time, Retail on those things was only about 80 bucks less than what it was selling at new egg. Since I never turned in my rebate as well I only ended up adding about 160 bucks. Now one could argue that I payed 80 bucks more then I should of for that card but I got to use the 7900 and basically lose NO money on that purchase witch more than offset any losses of paying retail.
So yes do you pay retail, but you dont lose any of the value of your original purchase.
*I do miss my ol 7900gs though. I overclocked the piss out of it knowing that I would be returning it and was really happy with its performance. I got 7.5k 3dmarks from it with a e6600.
BTW OP, I was number 2 in the que when I started and it took over a month-yes a month- for the card to ship and for them to process my order even though they were more than willing to take my money right away. Dont expect it to be all done in a week like they say in the documentation.