In order to rename a Windows system remotely you need to use the NETDOM command:

The command has been knocking about for a while now and is standard in Windows 2008. In Windows 2003 you can find it in the Windows Resource Tool Kit

Example:

netdom renamecomputer old_name /newname:new_name /userd:domain_admin_login /passwordd:domain_admin_pwd

netdom renamecompuer domold-W7 /newname:domnew-W7 /userd:administrator /passwordd:Passw0rd