Well, first you should write to FeedBooks support: firstname.lastname@example.org
pointing to this thread. I'm sure they'll like to fix it.
In the meantime, fixing the ePUB is easy:
1. Unzip the .epub file, just as if it were a .zip file. If needed, rename the file to .zip first.
2. Open the OPS/fb.opf file with a text editor (not Word, but something like Notepad), and delete the offending opf:scheme="URI"
3. Add the modified file to the original .epub/.zip (or a backup). With WinZip/WinRar it's probably as simple as drag&drop.
4. Rename the .zip back to .epub if you had renamed it first.
5. Check it in the online validator: http://www.threepress.org/tools/
With something like WinZip/WinRar it could be even simpler, they might let you edit the files that are inside the .epub without having to actually unzip it.