It might seem very harsh however I can understand why they have done it. I was lucky enough to experience many jumpseat rides and quite a number of them were down to me providing my PPL with a little note for the guys up front, whenever I boarded. I have to say that it nearly always worked! However if you have a terrorist who has a PPL then that brown book is providing that person a path to controlling an aircraft with many people on board. I very much doubt if we will see it again - which is a great shame!
On the other hand having a genuine jumpseat traveller can actually boost security, in certain circumstances. Try barging into the flight deck on a 737 for example when you have a bloke who is parked on the jumpseat. You ain't gonna get past in a hurry!