I don't think the letter says don't take Court proceedings, it says make sure you've pursued all other avenues first, which he had not, and sue the MoD, not JPAC, who are just another office within the former.
As for Shackman commenting on the seniority of the 'legal personage' who replied, I'm not sure many lawyers would volunteer free advice to the plaintiff on how to do it properly next time, unless there was a degree of sympathy somewhere.