I don’t know exactly what your tree roots look like, but this thread from last year might help ease your mind: Burnt Ridge Rootstock Debacle - Rubber Bands are Not Expensive - #41 by krichberg
Krichberg and I both got some trees from One Green World that had some roots that were rather moldy looking. My two trees both came out of it fine though. I’m not sure how his did. So it may not be to dire, if yours look like ours did last year.