You can delete the configuration file (which is named Configuration.ini). Where it is located depends on your Windows version.
For Windows 95/98, the file is located in C:\Windows\Application Data\Spybot - Search & Destroy\.
For Windows ME, the file is located in C:\Windows\All Users\Application Data\Spybot - Search & Destroy\.
For Windows NT/2000/XP, the file is located in C:\Documents and Settings\All Users\Application Data\Spybot - Search & Destroy\.
For Windows Vista, the file is located in C:\ProgramData\Spybot - Search & Destroy\.
Either delete that file, or edit it (for example in notepad), and set all the Automation values in it to zero.
You can download a small tool that will do those changes for you:
click here.