I notice - when viewing a custom attribute, there is no option to delete it... only view the properties?
Apparently this is by design. There is no harm in having "extra" attributes in SCOM - that arent used. However, if you do want to delete an unused attribute - you will have to export your MP - and then edit the XML, and reimport the MP:
Export the management pack to XML. Then open it with XML notepad, or your favorite XML editor, and delete the section defining the attribute.
Or - a simpler method - find the object discovery for the attribute in the Authoring pane of the console, and disable the discovery that was created for this attribute.