I have not tried some of this stuff, but if you are in the command prompt, did you go to the C: drive before you issued a command?
This site talks about using a command line to restore the registry, but I am not sure if they are talking about your situation. Tell me exactly what command prompt you are trying to import the registry in and I will do some testing. If you can't get into Safe Mode, is suppose it also means you cannot get into Safe Mode with Command Prompt?
I do know you can edit a registry hive from the WinRE command using the Regedit
Load Hive option. If you want to get into that, I will try to find the information if you like. I think the problem is the registry used in the WinRE is a virtual registry and does not effect the actual registry files.
Only the HKLM and HKU hives can be done this way, so if your problem is not there, it will not help.
Does the Cleaner have something you could boot to or use from a command prompt to restore that file? Can you open the log the Cleaner left to see what it might have removed?