Best way to protect a MOSFET from overcurrent
This is a problem when you use something like an MCU to control a device which exists on the edge of blowing up, depending on timing, since the MCU can lock up from EMI or whatever (even when the firmware is working perfectly) and destroy the MOSFET and/or transformer. Hardware-based circuits are less of an issue. 

An ordinary watchdog timer may be insufficient to protect the MOSFET. During development you could rig something (like a one-shot and gating) that would limit the on-time of the MOSFET but that's probably not practical for a production circuit. 

I have used the nonlinear characteristics of a tungsten light bulb as a series resistor during development. Depending on the actual currents involved, you may be able to use an incandescent automobile lamp (interior lamp, brake light or even a headlamp) as a series limiting PTC (positive temperature coefficient) resistor during development. If the light illuminates, you have a problem.