Close call. Depends on how you like the frame, really. Have you had an opportunity to ride a 4.7?
The Lemond was a good frame, so is the 4.7. I honestly feel the 4.7 TCT carbon frame has slightly better and newer technology that is present in the 5 and 6 series designs from 2008/2009. Even though the Madone fork is a RL, it has the E2 steerer, something the Lemond lacks. Plus it has the integrated Duotrap thing for wireless computers which is pretty cool. I would take the RL E2 fork over the older style RXL fork any day. It is stiffer and stronger, and it might even be lighter. (While the 4.7 doesn't have the integrated seat mast and the integrated BB shell, neither does the Victoire.) To me the Victoire was an older design in its last year(s) while the 4.7 was a new design and benefited from new tech. Lastly, you are getting a brand spanking new carbon frame and fork, that is fairly high end (presently), in exchange for a 3 year old frame and fork that was fairly high end (3 years ago).
If you feel shorted, ask them to throw in a new duotrap compatible computer and sensor.
You will be able to swap over your components and kit to the Madone, so that is not an issue.
All in all, I don't think you are getting shorted, but if you feel you are, then I would press for something better, and see what happens.
HTH a little
zac