I've had a thermocouple outside on my grill connected (remotely via CAT5 cable) to my HM for about 10 years now. I cook low and slow but also cook pizza as high as 700 degrees. I killed a dozen regular pit probes before I switched to thermocouple, never killed a thermocouple, so I disagree with your assessment. That said, being a permanent connection I don't unplug the TC often, so maybe that's why I don't have issues with the TC wires.
Due to the high heat insulation on the TC wires, twisting and turning the cables can cause wire to become exposed and short out, but it's an easy fix. I learned to pull back the insulation , cut the wire short, then connect it to the screw. This makes the insulation kinda push itself into the connector and prevents exposed wires. There's no way a regular probe would survive the heat and weather I have put my TC through, so I am TC all the way for pit probe....
That said, you have two options.
1) In the HM config, Disable probe 0 (TC) and probe 1 (regular) will now become the pit probe. You lose a probe, but I rarely use all four probes anyway
2) The HM board does have holes in place for a standard probe socket at probe 0. You could install a regular probe jack there if you like. You'd have to look at the TC circuit on the schematic and find the component or trace on the board that leads in/out of the TC circuit and either remove the first/last component, or strategically decide a couple traces on the board to cut to disconnect the TC circuit... Oh, and you'd have to install a pullup resister and I think a filter capacitor there at probe 0 as well, there will be holes on the board to install those parts.
My advice to you would be to get better at connecting the TC wires in a way that the insulation doesn't pull back on the wire, and make sure you do not omit the red rubber ring, it seals the connector and also helps squeeze the wires and hold them in place. If connector issues plague you during cooks perhaps just buy a spare TC so you can swap them out real quick and fix the connector later?