You can clean out any numeric directories under the uploads directory via ftp
The link on upload to the que should process the images. The code if an image dies before processing it should be deleted however that is dependent on the script actually running. If your php is dieing on the server there is no way to remove the image but ftp. That or use Imagemagick as your processor since GD2 is ultimately the issue as that image processor can not process huge images.
My suggestion would be to clear your que via ftp and if you can not use Imagemagick make sure your image sizes in admin are sufficiently low enough not to cause GD to freak out.