For now your choices are to add an inverter such as the transistor circuit you mention, or try to create a Lua script that changes the polarity of the PROBE input. I don't *know* that this can be done in Lua, but I see function calls that should make it possible. See the Mach4HobbyDocsMach4CoreAPI.chm file and look in the "API Reference by Category", then in "Mach Signals" for functions mcSignalGetInfo and mcSignalSetActiveLow. You will most likely need to make sure Mach4 is disabled when you call the "set" function. And there may other functions you need to call, such as in the "GUI" section, the ncCntlConfigStrart (before you can call the "set" function) and mcCntlConfigEnd (when you are done making changes).
There is a facility in Mach4 to support multiple probe inputs (4 in total), with each one able to have its own active high/low setting. On the Mach4 configuration dialog in the "Input Signals" tab there is a "PROBE" input, which you are currently using. If you scroll further down you will see "PROBE1", "PROBE2" and "PROBE3". The G31 command uses the "PROBE" input. Mach4 added "G31.1", "G31.2" and "G31.3" variants to use the "PROBE1", "PROBE2" and "PROBE3" inputs, respectively.
Alas, the SmartBOB plug-in does not yet support the additional 3 probe inputs nor the G31.x variants.
Bob