I wouldn't chop off the roots right away. I'd do like suggested, hydrogen peroxide (h2o2) 3ml/gal of water. That should clear it up. I'd do that first and go from there. It will not effect your plants negatively either. However, I guess cutting off the bad roots won't hurt either... You do need to use the h2o2 though.. They also make a product for root rot called hygrozyme, or something like that. You can look it up..
-S