lucy24 - 6:25 am on Sep 21, 2012 (gmt 0)
my gut feeling is simply to delete it
You mean delete the non-canonical domain from wmt? No. It will just come back. There's a place in gwt where you tell them your preferred name. Once they've assimilated it, future SERPs will eventually give only that form.
You also need to make sure there's a redirect in place from all wrong forms of your domain name to the one right form. That's in htaccess or config, not in gwt. There are, at a rough guess, eight thousand posts in the Apache forum telling how to do it. Or, if you're on shared hosting, you can cheat and let your host do it for you. They should have a checkbox somewhere.