In SharePoint MOSS 2007 if some sites become messed up for whatever reason you will not be able to access the site and hence not delete the site.
Normally you open/access the site choose Site Settings->Delete this site. If the site is not accessible you can type in the path to the delete page manually
note you have to use the full path, the parentsite/…/sitename. All other pages on the site should also be accessible this way; you can find the path by using a site that works and just substitute the path for your problem site and hopefully it will work.
(Another option is to write a small program to clean up or do your bidding)