In January this year I was on a DJ flight flying on a 737 SYD-CNS that had 2t of excess fuel/was 2t overweight, DJ spent 30-45min trying to find a fuel pump and apparently SYD airport doesn't have one... They ended up taking IIRC 14 passengers and their bags off the flight (8 being carry on only passengers). In total was a 1.5-2 hour delay. Not sure why or how the plane ended up with 2t of extra fuel, flight wasn't completely full, maybe had like 5 spare seats in Y. (I think the Captain mentioned something about reduced thrust levels but can't remember exactly)
Defuelling doesn't happen very often. I've never been had to do it, but I'm told that it's a much slower exercise than putting the fuel on. Most overfuels are quite small amounts, and in large aircraft a few hundred kilos can be 'off loaded' by the simple expedient of burning it. That's not really going to work when talking 2 tonnes and a 737. The 380 would go through that in about 40 minutes with all engines at idle and APU running.
On any planned operation at max take off weight, the loading has to be very carefully stopped at the right level, and you then need to ensure that you do burn the planned taxi fuel before take off. MTOW is limiting at the START of the take off run.
Most overfuels that I've heard of haven't really been overfuelling at all, but rather a change in the tasking of the aircraft after a fuel order has been loaded. Suddenly changing an aircraft that was doing a 4 hour sector, to a 2 hour sector will often cause issues.
Remember too, that the crew are considering not just the MTOW, but the max landing weight as well (WLW). That often places a maximum on the take off weight which is well below any performance limits (MTOW cannot exceed planned burn plus MLW). The combination of MTOW and MLW with weather holding requirements (which increases the amount of fuel you need on board at the end of the flight) complicates things further.
I don't understand the comment about reduced thrust levels. That should not be relevant to any weight decisions...you use whatever level of 'reduced' thrust you NEED for the weight offered. Performance weight limits could come into play if the aircraft were being forced to use the shorter runway in Sydney for reasons of runway works, or any other non wind related reason. If you have to use the short runway because of crosswind on the main, then that wind itself tends to give back much of the performance lost by changing runways, but if it's a very strong, but gusty wind, then that may impose a performance limit.
In any case, the fact that they were prepared to remove the fuel indicates that they didn't need it, so I'd expect it was either an incorrect fuel order that was loaded, or an aircraft change.