Here's the core subroutine for one I created and used in the past. It was 2004 when I last edited this one, but it should still work for ConfigMgr 2007. As always with scripts, be sure to test it thoroughly in your test environment first.
The premise of this subroutine is that you've built a list of boundaries you want in the boundaries array - that would be all of them without the ones you want removed, in this case. It also assumes you're only using IP subnets as boundaries, but it would
be easy to adapt it to handle the other kinds of boundaries.
The SDK has more background on scripting site control file changes.
Set WbemContext=CreateObject("WbemScripting.SWbemNamedValueSet")
WbemContext.Add "SessionHandle", WbemServices.ExecMethod("SMS_SiteControlFile", "GetSessionHandle").SessionHandle
WbemServices.ExecMethod "SMS_SiteControlFile.Filetype=2,Sitecode='" & Site & "'", "Refresh", , , WbemContext
'WbemServices.ExecMethod "SMS_SiteControlFile.Sitecode='" & Site & "'", "RefreshSCF", , , WbemContext
Set WbemInst = WbemServices.Get("SMS_SCI_SiteAssignment.Filetype=2,Itemtype='Site Assignment',Sitecode='" & Site & "',ItemName='Site Assignment'", , WbemContext)
'Retrieve the boundary details
proparray1 = WbemInst.AssignDetails
proparray2 = WbemInst.AssignTypes
duplicates = 0 : added = 0
for i=0 to numboundaries-1
boundary = boundaries(i)
boundary_type = "IP Subnets"
if boundary<>"" then 'as it would be if it was found to be a duplicate
onemore = ubound(proparray1) + 1
redim preserve proparray1( onemore )
redim preserve proparray2( onemore )
proparray1( onemore ) = boundary
proparray2( onemore ) = boundary_type
added = added + 1
else
duplicates = duplicates + 1
end if
Next
WbemInst.AssignDetails = proparray1
WbemInst.AssignTypes = proparray2
WbemInst.Put_ , WbemContext
'WbemServices.ExecMethod "SMS_SiteControlFile.Sitecode=""" & Site & """", "CommitSCF", , , WbemContext
WbemServices.ExecMethod "SMS_SiteControlFile.Filetype=2,Sitecode=""" & Site & """", "Commit", , , WbemContext
WbemServices.Get("SMS_SiteControlFile").ReleaseSessionHandle WbemContext.Item("SessionHandle").Value