How to read audio from a 3.5mm jack?
You are on the right track. It is very unlikely that over-voltage audio signals will cause any kind of "damage" to the CPU or the ADC. The worst that can happen is that the signal will be "clipped" or "flat-topped" which will cause distortion.  So you can write the firmware for your application to look for an extended sequence of minimum (zero) or maximum (your did you reveal your digital resolution?) and reduce the gain of the input stage. Or conversely detect an average audio level that is too low, and increase the gain, etc.  You may be anticipating "problems" that aren't really "problems".