Disconnecting the battery will not harm anything. You will need to have the code for your radio though. Once disconnected it will go into "SAFE" mode and the only way you can get it work is to put the correct code in. If you don't have the code, bring your car to a dealer and they can look it up for ya.
As far as clearing the CEL, just disconnecting and reconnecting the battery will not usually clear a DTC. I would strongly recommend having your car scanned by someone with VagCom, or by an auto parts store that may be able to do it. Use a dealer as a last resort since they will charge you $$$ just to scan it.
Good Luck
