If it's fowl pox (and that's what it looks like to me), isolating the rooster doesn't mean your hens won't get it, because the virus is transmitted by mosquito bites. The fowl pox scabs are infective, too, so that's why isolating the infected bird is recommended on the off chance that another bird might peck up a scab (yuck) and then come down with the "wet" form of pox...this is when the lesions form inside the trachea and/or esophagus. The dry form (when the lesions are only on the comb and wattles, sometimes the legs) is usually not serious and the bird recovers with no problem.
All my flock came down with it last fall, including our roo who developed the wet form, but all of them recovered. The virus is not contagious to humans and the eggs are safe to eat, but hens frequently quit laying while they're sick with fowl pox anyway.