that's normally why people scrub the rock. to get rid of algae. unless it's new rock that hasn't fully cured. but, it won't hurt anything to scrub away if you wan't to. just be sure and rinse in fresh saltwater before placing it back in the tank or you will re-introduce everything back into your'e tank. i normally use used tank water after a water change to scrub the rock in. it will help from wasting several gallons of saltwater to clean the rock in.
Yes I meant only scrub areas where you have nuisance algae problems. If it's new rock areas with questionable sponges might also benefit from a cleaning.
The rest of the rock I'd leave alone. No need to remove possible interesting organisms growing on the rock.
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