The algae growth could be caused by a phosphate build-up. If you stirred it up now, you would just release all of it into your tank. If you want to deal with the problem now, make a judgement of how well your tank inhabitants can deal with the disturbance. Stir it up while running a phosphate sponge in your filter.
I don't have a sand bed in my SPS/Clam tank, but I still apply the 'hurricane treatment' once a month. Either with a turkey baster or powerhead, you can direct currents all over your rockwork conjuring up all the settled detritus. If you have a sand bed, you'll want to unearth as much of that detritus as you can. This simulates the natural occurence of storms. Simply run your filtration with filter media (floss, carbon, phosphate sponge, etc.) temporarily to collect everything. Some even run an extra canister filter while doing this.