How to properly couple an audio (headphones) signal from a big/unknown system (worried about short circuits and ground loops)
Since most headphone outputs need to drive headphones of various impedance, they often have a quite low output impedance. 4 Ohm or less is typical for output impedance on a phones jack. This should allow you to add any high input impedance audio amplifier into the circuit in parallel with you headphones without any worries about overloading the output. Having said that, I'm a bit doubtful that a cockpit intercom follows any consumer audio conventions. I would recommend having a look at the signals with an oscilloscope before designing any circuits. Isolation is going to be important, and you'll also want to scale the signal to match your analog conversion input. depending on your flavor of ADC, you might need some signal amplification in order to get the maximum dynamic range out of it. If the phones output follows typical Line-Out conventions, the signal will typically be below 1.2V P-P at it's loudest (your pain threshold).
There is a guy that already makes the device you probably want. Here is a link - https://www.crazedpilot.com/audio-recording-cable-for-your-iphone/
This device has a 3.5mm TRRS output plug. I'm not sure about any isolation that they have implemented (or not) since they likely assume you will be plugged into a battery operated device that is fully isolated. Might be worth a look though.