They way I understand the construction, the Lowpass filter, which is what you are seeing, is bonded to the sensor, thus if Canon replaces it, they
are replacing the entire sensor, which for the cost you posted IMO is a bargin.
The other option would be to consider sending it to MaxMax, the company that takes off the low pass filters on 5D's. See their site for a detailed
view of the entire sensor and you can see the various layers that are all bonded together. They removed the low pass, which they claim gives the
camera better resolution. Since all you have is a scratch on the Low pass, you might consider their offering.
They quoted me around 700.00 U.S. two years ago to work on a 1ds MKI, I am assuming the MKII would be about the same. Note, it's not a reqular
conversion that they do, like the 5D.
They replace the lowpass with a optically clear piece of glass.
Paul Caldwell