You can use the COMAdmin.COMAdminCatalog object to remove components from a COM+ Application. You can do it through powershell or vbscript.
Here is a powershell example for removing a specific component from a specific application.
$comCatalog = New-Object -ComObject COMAdmin.COMAdminCatalog
$appColl = $comCatalog.GetCollection("Applications")
$appColl.Populate()
$app = $appColl | where {$_.Name -eq "COMAPPNAME"}
$compColl = $appColl.GetCollection("Components", $app.Key)
$compColl.Populate()
$index = 0
foreach($component in $compColl) {
if ($component.Name -eq "SOMECOMPONENT.NAME") {
$compColl.Remove($index)
$compColl.SaveChanges()
}
$index++
}