You're lucky to have a camera that has a usable auto-ISO mode. The lack of one is my favourite gripe about the 5D II.
I don't quite understand your question. Changing the ISO is just another way of adjusting the exposure; doubling the ISO will have the same effect as halving the shutter speed, except that it will increase the amount of image noise. I don't see why using a polarizer should cause any special problems.
If you're in doubt, you could always take a few test shots and see how they turn out. It's not like we have to worry about wasting film anymore.