The following example shows how you can delete an existing website:
[C#]
| using CMS.SiteProvider; using CMS.CMSHelper; using CMS.WorkflowEngine; 
 ... 
 // Code name of the site string siteName = "mysitecodename"; 
 // Delete records in CMS_Tree and CMS_Document DocumentHelper.DeleteSiteTree(siteName, null); 
 // Delete other dependencies and the site SiteInfoProvider.DeleteSite(siteName); 
 lblInfo.Text = string.Format("Site '{0}' has been deleted.", siteName); | 
Page url: http://devnet.kentico.com/docs/devguide/index.html?delete_web_site.htm