If you unplugged the amp from power, the protection light (or any lights) wouldn't be on. I'm having a hard time understanding what you're trying to say here.
99% certain that a head unit swap isn't going to help you at all. Protection light means bad stuff, period. If anything equipment related I'd say maybe you have an amp going bad and causing voltage spikes or back-feeding power somewhere. My money is still on wiring, though.
Car audio stuff is really hard to diagnose over the internet. If you can't get it figured out, just take it to an audio shop. They'll have it diagnosed in an hour.
EDIT - The only way I see this being a head unit issue is if you're getting voltage spikes over the RCA cables somehow, but in all my years messing with this stuff I've never seen one fail in that manner.