Because the usual UK government rule of thumb is to take the most economic route there - this usually means not flying BA, particularly for the regional based staff. Additionally, for regional based staff, flying BA down to London to connect was also seen as an extravagance, and since going by train and connecting across London was too much like hard work, most people I knew travelling ended up on KLM or LH. Departmental rules on premium classes also varied a lot - departments with lots of staff flying generally had reasonable rules (DTi, FCO), whereas for those where most staff didn't travel overseas routinely, travelling overseas was viewed as a holiday (no matter what the work involved), so all economy was the norm.

The one route I know of where BA was used without a second thought was GIB. There's some agreement between MOD and GT on that route.

Collection of miles and points is still a no-no in some parts of the civil service. Just before I left, a memo was sent out reminding us we were not to do this (or if we did, any points/miles accrued must be used for official business), but they did graciously allow us to use the perks of any program we held status in while travelling on business That memo was a triumph of someone writing about something they know absolutely nothing about. I wished I'd kept a copy!