Hi,
This is an interesting question. But once you boot to WinPE, there is no way of asking Ghost not to image it. On the other hand, even if you block overwriting it from one application, it may not work for others (for example running diskpart and clean the disk or using a different imaging product).
I think one option is to limit the bootability from devices. Most of the BIOSs allow you to specify the boot sequence to boot only from the hard disk as well as not to display the boot menu even if F12/F8 is pressed. Depending on your situation, you may use a Administrative password also in BIOS so that these cannot be changed without authority. Since OS always protect the system drive, it should be safe.
I too would really like to hear if there are other ideas.
Krish