It is highly recommended to design any system that supports hot-plug connectors such the ground and power contacts are mated before signal contacts. For example, the USB connector was designed to support hot-plug and it connects ground and power before the signals.
I understand you may be forced to use an audio connector that was not optimized for hot-plug, but your system solution must compensate for issues created when not using an optimized connector. As you mentioned, it may be necessary to add additional circuits that will guarantee the voltage applied to AM335x terminals remain within the recommended operating range.
Have you monitored the current flowing into the respective VDDSHVx power supply rail when the GPIO pins seems to be frozen. If you over voltage the GPIO enough to trigger a latch-up condition the VDDSHVx power rail supplying power to this GPIO should increase and will remain until power is cycled. You cannot clear a latch-up event with reset.
Inserting a series resistor will limit the current for this over-voltage condition and is likely to reduce the chances of triggering latch-up.
If this injects enough noise you may also be causing noise to be coupled into the crystal circuit which can glitch the reference clock. Please read Advisory 1.0.30 in the AM335x Silicon Errata.
Regards,
Paul