A GA aircraft doesn't have to be full of terrorists to be a "threat".
Surely a more plausible threat from a GA aircraft is to accidentally bust airspace and then fly blindly near/through a scrum of media helicopters, police helicopters, UAVs, etc. I remember Dale Farm got NOTAMed for that reason and, sadly, I think the Olympics will be an even bigger nuisance than Dale Farm was. Shutting down vast areas of airspace is overkill, but it isn't totally stupid to consider the threat.
But increasing the area of "shut down" airspace makes it more likely that some will be "busted" because there is more to
be busted. Much of the scrum of other aircraft will only be there to look for airspace busts.....
We are already in a situation where crews of private aircraft are being frisked and having their bags X-rayed on the apron. It's happening now! God help us when the Olympics restrictions actually begin.