It would be a mistake to run a skimmer on a timer. Skimmers require a good slime coat to work at optimal levels. Thus the reason that all skimmers require a break in period to get settled in. Some skimmer can take a week or more to break in. If you shut your skimmer off for any reasonable length of time, the skimmers reaction chamber and neck will dry out. The end result it that again, the skimmer will take some time to settle back in once it's fired up. Maybe not as much time as a new skimmer but it certainly will not run at optimal efficiency for several hours or more.
Having said that, skimmers are designed to be run 24/7 and not intermittently. If you are worried about the noise, get yourself a good skimmer that runs a quality pump.