Most newer diesels don't have a purely mechanical fuel pump, there is an electrical cutoff somewhere in the system. When I first started in the fire service everything was mechanical and the only way to stop the diesel engine was to pull the fuel shutoff knob. I have never seen a runaway situation where a fuel shutoff would have stopped the engine. It was always caused by another fuel source such as natural gas, oil, or spilled products. As others have said cutting off the air is the only solution.
The fuel shutoff did come in handy when one of the firefighters was backing a 1970 Mack up the ramp into the station and lugged the engine down to low RPMs. It was in reverse and rolled forward causing it to start running backwards. Fuel shutoff came in handy then.