Is there a way to disable the E-stop trigger when a file is loaded? I am using Mach3 on a Reprap style 3d printer, and control my heated elements with the spindle relay. When the E-stop is triggered, I have to wait for my heater PID controllers to cycle and come back to temperature.

Sounds like you may be getting a watchdog error, if so disable it on General Config.
Hood

I have watchdog disabled.

Think I've got it by unchecking 'Turn Off Spindle' under Pgm End settings, and can add a M5 at the end of my gcode to turn turn off the spindle relay/heaters.