Leather soles are gonna turn black/grey/dark from wear anyways. I'm like you though, somewhat of a germ-a phobe. Unless anyone here says otherwise, I'd spray the soles with Lysol to disinfect, being careful not to get it on other parts of the uppers. Leather soles are like sponges sopping up anything liquid. However, I'd still wear them without babying them too much.
You could go with a nice pair with commando soles; they're hardly noticeable...
Hang in there and enjoy your shells my friend!
looking good in your wt