Oh dear... I had terrible problems with LECA pellets with my vandaceous orchids. Now, I wasn't doing semi-hydro like you are...I just wanted to use the pellets to stabilize the roots, but I had the same problem...any of the roots touching the pellets turned black and yucky. There was even fuzzy stuff on the pellets themselves. I've heard of other people having similar problems with straight LECAs.
The first thing I would do to clean up those poor roots is give the plant a good bleach bath. 9 parts water to 1 part bleach. Soak the plant for a few minutes (I tend to soak mostly the roots and sort of "prop up" the rest of the plant,) then run clean water over everything to clean off the bleach solution when you're done.
I've also done hydrogen peroxide on areas that have looked particularly bad, even after bleaching. The fizzing and bubbling from the HP kills any other nasty little buggers that might be hanging around. If you've got gunk embedded in hard-to-reach places, try using a small pair of tweezers to remove any rotting material that has not already been washed away.
Once the plant has been cleaned up, let it dry out for a couple of days. When you rehydrate it, add a little bit of Superthrive to the water you are soaking it in, and that will give it a little boost. Don't forget...when you're doing semi-hydro, the plants have no source of nourishment except what you give them, so if you've been holding off on the fertilizer, they might be suffering from lack of nutrients as well.
Finally, I would just ditch the whole s/h thing all together for this particular plant. I would prop it up in some good clean bark and mist the base of the plant daily to wet the areas where the new roots will emerge. Don't soak the media completely, because the plant doesn't have enough roots to absorb all the moisture yet, and you'll end up with more stagnant water and possibly fungus.
So, in a nutshell, give it a bleach bath, use hydrogen peroxide on anything else that looks particularly yucky, pick out any rotting bits with tweezers, let the plant dry out for a day or two, then rehydrate it in a bath of water and Superthrive. Prop up the plant in some bark (it will need support because it doesn't have the root system yet to hold it up), and mist the base of the plant daily. You should see new root growth fairly quickly.
I would advise not using the s/h LECA pellets on this guy, though. The only thing I use the LECAs for is to keep my bark from compacting too much in the cooler months. But LECAs by themselves have always spelled disaster for me! LOL
Okay...I hope this was helpful. I'm just sharing what has worked for me. Oh, and Physan is great stuff too...with regular treatments it will keep the mold and fungus from developing in the first place. :-)
Other forum members, feel free to chime in here if I've said anything that doesn't make sense... I'm just sharing what works for me, but I know there are a lot more experienced growers on here!