If you have the strong desire to avoid iron discoloration and the funds to filter the amount of water that your pond requires...filtration is and option, albeit an expensive one that requires periodic maintenance. I would not even venture a guess as to what a filtration system would cost for this type of application and lean towards embracing the "natural" discoloration of the rocks.

Now that I re-read your post. It sounds like you are recirculating water from the pond to the water feature. I will assume that the pond does receive most of its water from a watershed and that it is not wholly coming from the well. If this is the case, the iron staining will be minimal once the pond is full and filled more by mother nature than the well. Consider holding off on running the water feature until the pond is full and stabilized.

The rocks will develop staining to some degree. Minerals in the water, of course, bacteria's, algae, silts, etc will all play a roll in how they patina.

I'd say embrace what ever happens...it's sounds beautiful...how about some pictures?

Welcome to PB, btw!