I'm an upgrading user and have my bookmarks in ~/.opera/bookmarks.adr. Default bookmarks seem to be stored in /usr/share/opera/defaults/bookmarks.adr or /usr/share/opera/locale/<LANGUAGE>/bookmarks.adr. The files are plain text. It may not be a perfect solution, but I think you can just edit it to remove them. (Make sure Opera's not running while editing, of course.)
I'm an upgrading user and have my bookmarks in ~/.opera/bookmarks.adr. Default bookmarks seem to be stored in /usr/share/opera/defaults/bookmarks.adr or /usr/share/opera/locale/<LANGUAGE>/bookmarks.adr. The files are plain text. It may not be a perfect solution, but I think you can just edit it to remove them. (Make sure Opera's not running while editing, of course.)