Latest nightly !GNUsocial will move all your thumbnails into a separate directory ('thumb', which will be automatically created inside 'file'). I think I've managed to get rid of all the bugs related to it, but I'd like some beta testing please. :)
Also, to clean out your thumbnails to allow for regeneration (freed a couple of gigabytes on quitter.is :P), run 'php scripts/clean_thumbnails.php'. Any thumbnails of attachments you have should be linked as /attachment/$id/thumbnail (with GET parameters deciding non-default sizes)