I flushed the system as best I could, a few times. Then I filled it 50/50 with water and white vinegar. Took a few days, driving the car, but it came good. I wouldn't leave it in there much longer though.
It will clean up all the rust in the system, but it will also need a damn good flush after. You don't want the crap going through your radiator either, so an inline filter in the top hose is the go, even if it's just a stocking slid over the hose fitting.