I just remembered that when you use RSD or Matt's utility, you are in AP Fastboot Mode anyways, so booting into the phone's OS is not essential. So, if you could go into CWM recovery, do a Factory Reset, format the SYSTEM partition, turn the device off, and get into AP Fastboot mode, and attempt the restore to stock process. Maybe that could work?
The signed partitions preventing the flash are not in the/system directory. So wiping your system shouldn't do anything.