Apparently there are two possible ways to achieve this
by using the property setClickable(flag:boolean);
see http://code.google.com/apis/maps/documentation/v3/reference.html#Marker
Remove the listener off the marker. It will look something similar
to this
google.maps.event.addListener(marker, "click", function(etc)
Reference
Also, if you work on the map in Collaborate mode, at the upper right of the left frame (with the locations listed), there's an Edit button. Click it.
Then go to the location you want to remove in the list on the left and click it to open it's information window on the map (expanding from the droplet-shaped marker). Inside that information box is a "delete" link, and that removes the location.