I've just sorted mine out...it stopped working all together which was strange because it worked fine last year.
I personally wouldn't recommend disconnecting it as this has a direct effect on the main heating system and you'll also notice the engine doesen't get up to temperature.
The fault with mine turned out to be because the auxillery water pump under the bonnet had failed...this supplies the aux heater with a fresh supply of coolant for approx 5 minutes after the engine has been switched off to prevent the heater unit overheating.
The aux heater has an internal temp sensor that monitors coolant temp inside the unit, if it detects an overheat it shuts it down.
After 5 overheat shut-downs the fault is stored and the heater is effectively 'locked out' and until the fault memory has been cleared it WILL NOT WORK.
I replaced the coolant pump and also fitted a new glow plug as a precaution (£19 from GSF)
Mate at VW cleared the fault memory and away we go!!! Heaters now great and the car gets upto temperature in no time.