Just kick starting this thread. It took forever to get posted and didn't seem to show up as new.
I've been in similar situations like this. You're at a disadvantage on a couple of fronts: 1.) You don't have an ongoing relationship with the dealer, who I'm guessing is far away from you. 2.) The item they sold you is still working correctly, even though that feature may or may not have been the cause of the iPhone's demise. 3.) It's an unusual problem, and may have nothing to do with the amp at all. Especially if Marantz hasn't heard of it.
I think the only way you can absolutely guarantee some action on the part of the dealer is if you can prove to them that the Marantz is at fault. Which would mean sending it back to the dealer and having them troubleshoot, test, and potentially destroy another iDevice to see if they encounter the same problem. If they gave you a service agreement, they should do that.
If you are wanting to just buy a new amp anyway, maybe you can ask them to take the amp back and put those costs against a new amp that you buy from them and maybe they throw in a discount for your troubles? Cause you're never going to feel comfortable using that function again unless they can either prove it wasn't the cause or if you get a new amp.
Lastly, I'm not familiar with that particular Marantz, but typically those inputs aren't made for permanent source input. Just a casual plug and play. Sounds like you have (had) a dedicated iPhone for music, in which case I'd advise you to just get a dedicated iPod/iPhone doc that has a digital out and connect that to the amp's dac. It's more reliable and will probably sound better.
Follow up: Unit (SA-8004 -- which I mistyped in the OP) went back to dealer. They tested it and found the voltage regulator in the charger/USB port to be compromised. But they claim that it was most likely caused by the logic board in the iPhone going bad while plugged in. I don't know how they would know that, but logic board failure is the sort of thing that can happen to an iPhone.
Anyway, it has been sent to Marantz for warranty repair, and I should have it back in a couple of weeks. And then I guess I will decide to trust it with a iSomething.
Thanks for the input!