How can I implement a differential input for a logic analyzer probe?
The esp32 is capable of 27.2 ksps or 27kHz, so just about any instrumentation amplifier or operational amplifier would be fine for the purpose of subtracting channels, especially since the gain will probably be reduced to the 3.3V scale. 

The best thing to do would be to use a comparator stage after the instrumentation amplifier with a low noise DAC to set the reference for the comparator. 







simulate this circuit &ndash; Schematic created using CircuitLab