Currently there is only on way to delete factory connections - demolish the supplier entirely, rebuild and relink. The request is to add some means of unlinking factories individually, preferably in info window. When the player is public service, connection list could have also some sort of delete-buttons.
This is proxied from a thread (http://forum.simutrans.com/index.php?topic=6952.msg67258#msg67258) in Czech board.