I call BS. I haven't tried it but I would be shocked if EFI on rMBP did not support booting from a USB CD-ROM.
I suspect the customer support agent @ Apple that the OP spoke to was confused, or OP misinterpreted what he said. Possibly the CS agent was confused because Apple's own OS no longer ships on CD, nor (as of Mavericks) is it recommended that OS X be burned to DVD for installation. Possibly CS agent was confused because what Freyqq said is actually correct:
The Bootcamp drivers for Windows *used* to be included on the OS X installation DVD. It was partitioned such that if you put the DVD in the machine while you were running Windows, you would see Bootcamp installation files for Windows instead of OS X install files. So for Bootcamp, it used to be that you would install Windows from CD, then install Bootcamp drivers from OS X DVD while booted into Windows. Of course, again, as stated earlier, OS X no longer ships on optical media, so the Bootcamp drivers have to be installed a different way. That different way is to put them on a thumb drive and then install them from the thumb drive while you are booted into Windows. Either the Apple CS agent got confused because he knew something about this but he internalized that knowledge as "Windows itself has to be installed from a thumb drive", or OP misheard/misunderstood CS agent who was actually trying to explain this concept. (Since OP was complaining about a malfunctioning SuperDrive, though, I suspect the former. Maybe CS agent did not understand why OP was calling, though, only hearing "I'm trying to install Windows under Bootcamp" and missed the part about "my SuperDrive isn't reading the Windows install disc".)
Anyway, IF your SuperDrive is in fact defective, it should be easy to prove, and to get Apple to service it (assuming it is still under warranty), as long as you eliminate the Bootcamp part of it from the equation and just concentrate on the functionality of the drive itself. If you put the Windows disc into the drive while it is plugged into the computer and booted into OS X, can you see the contents of the disc? How about another DVD if not the Windows disc? Have you tried putting in a CD instead of a DVD to see if the problem is that it is having trouble reading one type of disc vs. the other? Have you tried hooking the SuperDrive up to a different Mac? (Which, come to think of it, would also be a great way to prove whether or not the problem is the drive or rMBP EFI's support for booting off of external optical media: plug your very drive into a different, older Mac, and see if you have the same problem booting off of the Windows install disc.) Can you borrow a SuperDrive from someone else and try it with your Mac?
Process of elimination, people.
-- Nathan