I really hate to be the one to defend TSA here (gasp!), but there is something accomplished here.

Yes, a pilot can crash his own aircraft, so there's nothing gained regarding the security of his flights. But the pilot could also be carrying contraband (knowingly or unknowingly; willingly or unwillingly) through the checkpoint which could be passed on to a third party inside the sterile area, thereby presenting a threat to some other flight.

Remember: part of the reason for the multi-hour debacle at EWR last year was that after Wrong Way Corrigan entered the sterile area through the exit, he was left unobserved for a long period of time. They fairly quickly figured out that he'd left the area, but didn't know if he'd done Something Dangerous(TM) in the meantime ... leading them to dump the whole terminal and search the place from stem to stern.

If you don't physically screen everyone who enters the sterile area, every time --- including TSOs, vendors, pilots, maintenance workers, and custodians --- then you have a built-in mechanism to introduce "contraband" (however you want to define it) into the secure area. Of course, TSA already declines to physically screen most of those I've named.

Either screen everybody, or don't bother screening anybody.