Need help troubleshooting after short-circuit, with heaters and thermocouples
It’s not clear to me how you are reading the thermocouples, but I suspect the cause of your disaster was a short between the thermocouple and the “hot” mains line causing current to flow through all the non-isolated analog bits back to the (grounded) computer motherboard. Insulation breakdown was caused by the heater/thermocouple assembly melting. 

That would not happen if you used thermocouple signal conditioners with isolation (cost would, of course, be higher). Solid grounding on the metal parts and fusing on the mains lines may or may not prevent such damage, but is required for safety. If your computer was improperly grounded it might have become energized at mains potential. The thermocouple wires must be insulated to the same standard as any nearby mains wires (for example with fiberglass sleeving)- melting that insulation could otherwise have a similar effect to a short in the heater/thermocouple assembly.    

It’s also quite normal to have an independent over temperature controller, usually a very simple reliable device. In your case it could be something like thermal fuses or stand-alone limit controllers.