Can you replace broken 100k thermistor with thermocouple - potentially blown analogue input as well
Thermistors and thermocouples are different animals.  A thermistor changes resistance based on the temperature at the junction.  A thermocouple generates a small voltage (mV range) which varies depending on the temperature.  Higher temps typically use a thermocouple because thermistors tend to not be as accurate at those elevated temps.

My printer uses thermocouples, and it appears that yours does also.  I'm not sure what you mean by "crushed", but you can check to see if the wires are shorted to the heat block or to each other.  It is unlikely that you've damaged the input to the control board by doing this.  Shorted wires can give the same readings as no thermocouple attached.  You can also get errors induced through ground isolation if wires are shorted to the heating block.

Changing this out for a different system with a different input amplifier sounds like a nightmare in the making, and I'd only attempt it if I could not fix the existing problem or find a direct replacement.