The cloudy water is a good thing; you've neglected the substrate so detritus has built up and the fish is kicking it back up into the water column. That is a win win, less maintenance for you (though little has been done it sounds like), food for the corals, and removal of excess to the sump/skimmer/what have you. In time, all of that will be removed and your sand will remain clean. Unless you have corals on the sand that are easily moved (e.g. on frag plugs), everything will be fine. I wouldn't trade my diamond goby for anything; does the intended job extremely well.