Removing a Primary Site in System Center Configuration Manager 2007 is not quite the same as removing a Secondary Site.
Basically, what you need to do is to de-attach the Primary Site from it’s Parent (The Central Site).
Here is how you do it:
Open the SCCM console:
Connect to the Site Database of the Primary Site -> Right-click the Primary Site and select Properties
Change from “Report to parent site:” to “Central site”
Press OK and the uninstallation of the primary site will start 🙂 If you connect to the Central Site, you will see that it will not be visible any more.