Handle the threat the way European airports do. Paris Charles de Gaulle Airport, where the so-called shoe bomber departed from, DOES NOT REQUEST SHOE REMOVAL for U.S.-bound flights, and does not send passengers to secondary screening if they fail to remove thick-soled shoes that don't set off the metal detector. No beep, no harassment.

At British airports, the security staff don't even allow passengers to put shoes through the x-ray machine. If you beep, you're wanded and the screener conducts a visual inspection of your shoes.

I've never understood why shoes with a 1" thick sole are supposed to be so much of a threat. It'd seem to me that a careful visual inspection of shoes (while the passenger is still wearing them) would show if they've been "fixed" to hide explosive material, if there's even enough room to hide explosives in one's running shoes.