Run a couple of swabs soaked with oil down it and then a good snug fitting bronze brush a few times. Run a couple of dry tight fitting patches down to clean the crud out and then have a look.
Do like Chuck says. Clean it and shoot it. It's really the only way to figure out what the effect of the rust (if it is rust and not just copper fouling as Elkhunter questioned). One of the most accurate rifles I've ever owned had a dark spot halfway down the barrel. It was a lightweight carbine that shot half inch groups. Sometimes the sum total of all the flaws is zero. I sure wouldn't write-off the rifle due to a fleck or two of rust.