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.
