You could import the kml file directly into Basecamp. It will probably come in as a track or two. Highlite the track (mine was named Latitude user) and select Get info which will open a window with all the points. If you have done a show on map then as you select the point it will highlight on the map. So just highlight the relevant point and delete it.
I am wondering if you have used multiple devices then you might get lucky and have a separate track for each device.
Another way would be to open the track in an editor and delete the offending points there.
Just a wild guess, and I've never done it. What about exporting the waypoints to a CSV and importing it into a spreadsheet (Excel) Than sorting the sheet. Select the lines with the coordinates and delete them.
