I was able to use updateFirmwareFromFile.sh to flash the SAME EXACT firmware version I was running.
This was the last version of the firmware, but I would assume the script has not changed.
The script is dated back in June
WDMyCloud:/usr/local/sbin# ls -al update*
-rwxr-xr-x 1 root root 8289 Jun 21 2013 updateFirmwareFromFile.sh
Regarding the concern of flashing only ONE side of the RAID, the MyCloud is designed to split the md mirror on upgrades. It flashes one side, boots the new code then re-mirrors itself.
Please read the code!!! 
Here is the log from my recent update, note it doing the HOT remove of the md mirror.
Preparing to replace sq 03.01.04-139 (using …/sq-030301-156-20131230.deb) …
isImage=true
Master package name: sq
sq-preinst: action=upgrade
currentRootDevice=/dev/md0
forked-daapd: no process found
disable lazy init
Restore raid device: /dev/sda1
Restore raid device: /dev/sda2
Prepare for upgrade pkg install…
mdadm: set /dev/sda1 faulty in /dev/md0
mdadm: hot removed /dev/sda1 from /dev/md0
Preparing FW upgrade image on: “/dev/md1”
preinst: currentRootDevice=/dev/md0
preinst: upgradePath=/mnt/rootfs
preinst: upgradePart=/dev/sda1
