Shawn - Ouch! Just shorting like that while the blades are moving means all the rotational energy, not just above the cutin RPM but everything down to zero RPM, is instantaneously spiking your genny coils.
Just musing aloud about things, presumably by the time one says Hey I Need To Stop This Turbine, the controller's already going to have switched in the normal divert load. So what if one had a second divert load connected across the turbine output (after the rectifier if the diodes can handle the instantaneous amps, before them if not) which one could manually switch in for emergencies? It wouldn't have to stop the blades as such, just put them into stall - I think!
Obviously if before the rectifier, you'd want to load all the phases the same and at once. I have a mental picture of three industrial-size power resistors in star config. Wonder how you'd switch them in all at the same time? Three SPST's in a row, I suppose.