Делаешь 2 VBScript Custom actions WebSiteInstallExecute и WebSiteUninstallExecute:
Обе запускаешь в Deferred execution блоке с msidbCustomAction
TypeNoImpersonate флагом.
Ну и естественно присваиваешь WebSiteInstallExecute и WebSiteUninstallExecute property соотвествующие значения в Intermeduate блоке.

'//  MSI Custom Action
'//    IIS web site Installation                   //
'//    Infopulse Ukraine                           //
'//    Oleg Nalyvaiko                              //
'//    oleg.nalyvaiko@infopulse.com.ua
'////////////////////////////////////////////////////
Const msiMessageTypeError = &H01000000 ' Formatted error message
Const msiMessageTypeInfo = &H04000000 ' Informative message for log, not to be displayed.
Const msiMessageTypeUser = &H03000000 ' User request message

Const msiERROR_INVALID_PARAMETER = 87
' custom error codes
Const msiERROR_IIS_SERVER_NOT_FOUND = 1800

Function Show_Message(msgType, msgText)

    if msgType <= msiMaxMessageType then
    
        Set record = Session.Installer.CreateRecord(0)
      record.StringData(0) = msgText
      Show_Message = Session.Message(msgType, record)
      
    end if
    
End Function

' ----------------------------------
' Uninstall web site
' Set WebSiteUninstallExecute property to the [_IIS_SERVER_NAME]|[_IIS_WEB_NAME]
' for getting parameters through CustomActionData in the deferred execution

Function WebSiteUninstallExecute()

    Dim ServerName, ApplicationName
    Dim sParameters: sParameters = Split(Session.Property("CustomActionData"), "|")
    if UBound(sParameters) <> 1 then
        Show_Message msiMessageTypeInfo "Invalid parameters " & Session.Property("CustomActionData")
        WebSiteUninstallExecute = msiERROR_INVALID_PARAMETER
    end if
        ServerName = sParameters(0) ' Session.Property("_IIS_SERVER_NAME")
        ApplicationName = sParameters(1) ' Session.Property("_IIS_WEB_NAME")

    Dim objIIS, objIISRoot
    Set objIISRoot = GetObject("IIS://" + ServerName + "/W3SVC/1/Root")
    If objIISRoot Is Nothing Then
        Show_Message msiMessageTypeInfo "Cannot found IIS server at " & ServerName
        WebSiteUninstallExecute = 1
        Exit Function
    End If
    On Error Resume Next
    Set objIIS = objIISRoot.GetObject("", ApplicationName)
    If Err.Number = 0 Then
               objIIS.AppUnload
        objIIS.AppDelete
        End If
        Set objIIS = Nothing
        Set objIISRoot = Nothing
        WebSiteUninstallExecute = 1
End Function

' ----------------------------------
' Install web site
' Set WebSiteInstallExecute property to the [_IIS_SERVER_NAME]|[_IIS_WEB_NAME]|[INSTALLDIR]
' for getting parameters through CustomActionData in the deferred execution

Function WebSiteInstallExecute()

    Dim sParameters: sParameters = Split(Session.Property("CustomActionData"), "|")
    if UBound(sParameters) <> 2 then
        Show_Message msiMessageTypeInfo "Invalid parameters " & Session.Property("CustomActionData")
        WebSiteInstallExecute = msiERROR_INVALID_PARAMETER
    end if
    Dim ServerName, ApplicationName, LocalPath
    
    ServerName = sParameters(0)
    ApplicationName = sParameters(1)
        LocalPath = sParameters(2)

    Dim objIIS, objIISRoot
    Set objIISRoot = GetObject("IIS://" + ServerName + "/W3SVC/1/Root")
    If objIISRoot Is Nothing Then
        Show_Message msiMessageTypeInfo "Cannot found IIS server at " & ServerName
        WebSiteInstallExecute = msiERROR_IIS_SERVER_NOT_FOUND
    End If
    On Error Resume Next
    Set objIIS = objIISRoot.GetObject("IIsWebDirectory", ApplicationName)
    If Err.Number = -2147024893 Then
        On Error Goto 0
                If LocalPath = "N/A" Then
            Set objIIS = objIISRoot.Create("IIsWebDirectory", ApplicationName)
                Else
            Set objIIS = objIISRoot.Create("IIsWebVirtualDir", ApplicationName)
            objIIS.Path = LocalPath + "\" + ApplicationName
            objIIS.SetInfo
            Set objIIS = objIISRoot.GetObject("", ApplicationName)
                End If
    ElseIf Err.Number = -2147463160 Then
        On Error Goto 0
        Set objIIS = objIISRoot.GetObject("", ApplicationName)
    End If
    On Error Goto 0
    objIIS.AuthAnonymous = False
    objIIS.AuthNTLM = True
    objIIS.DefaultDoc = "default.aspx"
    objIIS.SetInfo
    objIIS.AppCreate 0
        Set objIIS = Nothing
        Set objIISRoot = Nothing
        WebSiteInstallExecute = 1
End Sub