You should strongly consider Mathieu's words as he is one of only a few who has done the entire route more than once, and one of a handful who has done it both ways. What he did not mention is that on his first trip he took a BOB trailer and on his second trip he used panniers, primarily due to safety http://www.crazyguyonabike.com/doc/page/?o=57&page_id=310026&v=2h. I am not trying to tell you about the route or if to take a trailer or not but just to seriously consider his suggestion that the GD is not a place for a two-wheeled trailer.
For a good and informative read, read his journals on the GD (over on CrazyGuy). His first includes incredible pictures by one of his companions Auke.