I don't see why you couldn't use clones that are moldy. Of course it's not ideal, but if it's a choice between that and not using clones, I would definitely use moldy clones. You can make mold go away. I'm not sure about those roots of yours, but I am a little familiar with mold during the rooting process. I keep a humidity dome on, except for a few times a day, and I usually end up seeing mold in a couple spots here and there. Most often where a leaf touches the cloner. This doesn't mean I'm going to throw them out. I spray a little fungicide on them to keep the mold under control, and I pick out mold as soon as I notice it. You could also try to do away with the humidity dome and use an anti wilt product instead. A dome greatly increases the chance of mold, and removing it greatly reduces the chance of mold. Also hardening them as soon as possible will help fight mold too. As soon as they can stay out of the dome on their own, there should be no more problem with mold, unless you don't have adequate ventilation.