I did try to remove the folders from the command line. Can you please give me an example to escape the names?
First, you have to find out their 'real' filenames.
So do something like dir /s /b *.* >some.lst
Then read it in hex-capable editor, you'll see they may not be spaces, but for example 0xFF's.
Then try to reproduce them on the command line, enclosed in parentheses. On nt based system you may try del /s on the first directory.
BTW: Can you tell us what 0day warez you've got there?
I can not turn off the server - this is a live, active Web site.
You should at least change all the passwords and check if there are no additional unknown users, or if some default users hasn't got some new privileges.