I think this might help you understand what's going on.
What you are asking for though is going to be tricky, as the pre-boot system is stored on the boot drive. You can't just keep the EEPC MBR and expect things to work. The error you are getting means the EEPC MBR is still in place, but you deleted the pre-boot file system (by formatting C:) - "cleanly removing the EEPC MBR" is not going to help you achieve what you are trying to do.
saying that, to achieve what you ask - "How do I cleanly remove the EEPC MBR without touching the partition table", that can be achieved by using FIXMBR.
as I say though, I don't think doing that is going to help in your ultimate goal though.