Isolate two Arduino analog inputs
Try this: -







simulate this circuit &ndash; Schematic created using CircuitLab

D2 ensures that the signal on it's cathode is shifted to a largely positive value and D1 rectifies it. C2 smooths it and R1 allows C2 to discharge when the audio signal dies away.

You might also need to protect the analogue input with a zener diode across the input and ground but its value depends on your power supply rail to the MCU.

The reason your modified signal "read" your hand is because your equivalent of my D1 didn't have C2 and R1 and between cycles of audio the analogue input floated.