You can use the DeleteBackup method of the IIsComputer object to delete a metabase backup from a backup location.
IIsComputer.DeleteBackup BackupLocation, BackupVersion
| MD_BACKUP_HIGHEST_VERSION | Delete the highest existing backup version in the specified backup location. | 
<% 
  Dim ComputerObj 
  Set ComputerObj = GetObject("IIS://LocalHost") 
  'Delete version 1 backup. 
  ComputerObj.DeleteBackup "MyBackups", 1 
%>