I guess you could do something with a manual switch that can flip between the pit probe and another probe jack but you would have to cut the trace for that probe on the HM board and piggyback wires on the jacks to wire through the switch to the ATMEGA inputs...
Right now I have a switch that flips between the onboard TC amp and my external TC amp as the pit probe (signal injected through the lifted end of the RC filter resistor for the pit probe), and had planned to add another switch that will select between the TC (whichever is selected by the TC switch) and a standard probe jack. My plan was to use a panel mount probe jack mounted in a hole I drill in the case (instead of cutting the trace on one of the onboard HM probe jacks) If you are switching between a TC pit probe and a standard pit probe you will have to leave the pullup resistor off the HM board and use one side of a DPDT switch to switch the probe input and the other side to switch in a pullup resistor (to 3.3v) when a standard probe is selected. I have all the parts and drew up the circuit but I wanted to do the TC switch and TC to standard probe switch one step at a time, so far it's been: step 1, pause..... lol
As far as the software solution, I would (still) love to see that happen some day. Instead of adding the ability to rearrange the probes would it be easier to set it up so if you select DISABLED for the Pit Probe then the first food probe would function as the pit probe? Or maybe on the next HM you could add an optional switch that would swap the TC with the first food probe as the pit probe for a hardware solution rather than messing with the software. The HM builder could choose to add the the switch or just install jumpers to select the pit probe...