I can't see why an ipod should have any effect on the electrics at all, the power consumption is minimal. I think that this was just a coincidence, if the battery light came on that indicates that the alternator is faulty. The ipod only uses a few thousandths of an amp, the alternator can supply upwards of 100 amps. To run the battery down in 45 minutes wold require a discharge of of 50 amps or more which would result in a considerable ammount of heat - if not smoke and flames.

The car went in to "limp home" mode. Its has some kind of engine or eengine management fault.

I bet you stopped and turned off the car and then unpluggd the ipod. It was the turning off the engine that cleared it, not unplugging the ipod.

The fault will come back, (even with the ipod unlugged)