It's possible that it's one of the fans inside the case... unless you are certain it's the hard drive.
I'd open the system up so that you can get a better idea where the sound is coming from. At that time, you could try disconnecting fans if the sound comes from one.. Don't close the case if you disconnect ANY fans inside the system. Leave it running to make sure that was the cause. If it is, then contact Apple to have them send you a replacement fan. If they don't want to do that, then tell me what the fan size is (they are usually in mm, such as 60mm, 80mm and 120mm). You could probably take the questionable fan to a local computer hardware supplier and get the same size replacement for a few dollars (under $10 depending on the size). If you do that, get a major brand fan, such as Antec, CoolerMaster, ThermalTake, etc. Don't get some odd branded fan. Also make sure it's ball bearing, so that it will last longer and be quieter.