Well, I'm in Scott's book also

The best information I have on rust (or rusty root) is from the Ontario Publication 610. They say it is both issues. Basically, when seed is stratified and it is allowed to get too cold, -4 C or about 24-25 degrees F or if the ground/roots get below about 23 degrees (-5 C) the roots can develop rust.
This is the primary reason for mulching your beds. Granted, there isn't much you can do in the woods unless you wish to spread straw.
As for your current crop, I don't know what you can do for sure. Perhaps you can salvage some outright, and sell the rest at a discount. I think it is a little early to be digging, and maybe time will be on your side. If you selectively harvest only the larger roots, you might be able to minimize the impact of the rust on some of them. I"m not certain, but I'm thinking I've seen roots which were infected with rust which eventually cleared up.
Also, I should note that there are four fungicides which are now labeled for ginseng which are labeled to be effective for rust. I discovered this -it was new to me- when I was researching the 2014 Ginseng Fungicide Report
http://www.emeraldcastlefarms.com/Products/Fungicide.html As for the seed I sell, I've seen very minor amounts of rust in a couple years on the seedlings I sell. Maybe one of 200-300 would have a small spot of rust on them. But, by and large after I figured out that mulching and its effects on the over winter temperature on the beds has cleared it right up. It is definately not from the seed I handle. I've sold and planted this seed for about 12 years now and I can't say enough good itthings about the grower who produces it. Not only does he produce a top notch product (I wouldn't sell it if I wasn't), but he and his family are top notch people as well.