Tonic, no I think you are confusing two issues here.
The gear is often left down on circuit training to cool the gear.
The issue here is (probably) something different - to do with brakes capped / de-activated due to a fault / leak.
On a normal take off the brakes are automatically applied as the gear is retracted, this is so the wheels are not spinning as they go into the bay.
If a brake is capped off that particular wheel may still spin after take off, so the gear must be left down for min 2 minutes to allow the wheels to stop spinning. This procedure would mean the MTOW is reduced by 14.3 tonnes.
The other option is wait until the engineers come from from base to fix the leaky brake - a long option.
I don't know about performance out of LIN, but from Italy back to LHR I suspect that performance would not have been an issue at all and they may have even got away without leaving any bags behind. (It's an overpowered beast....) To give you an idea, anti skid inop is a similar performance problem (13 tonnes degradation), and I made it make from SSH (Sharm - el - Sheik) to LGW a few months ago no problem....