I stir all the time. I find that if you do just the surface, one section a night, your BB will be able to handle it. I've been doing it for awhile and all is well. At first I was nervous because of what everyone always says, but I have seen no ill effects because of it. I know that my LFS
owner, before his monthly water changes, does a quick stir and then a water change. I have never seen an algae outbreak or anything bad come cause of it. He doesn't even run a skimmer, or a sump/refugium. Just simple filters. I won't advise you to do it, because I don't want to be blamed for anything that could happen, but I just thought that I'd share that I do it regularly and my reef is thriving.