There are two ways to delete a key from the Registry from the Command line. At the Windows Command line:

RegEdit /l location of System.dat /R location of User.dat /D Registry key to delete
You cannot be in Windows at the time you use this switch.

Or you can create a reg file as such:
REGEDIT4

[-HKEY_LOCAL_MACHINE\the key you want to delete]
Note the negative sign just behind the[
Then at the Command line type:
1. RegEdit C:\Windows\(name of the regfile).