For a kick-off this is not pay rises we are talking about - it is bonuses.
Most MOD civil servants have had the opportunity to earn a bonus by delivering fully against the targets set in their annual appraisals. The system has been running for about 6 years and is deeply unpopular with the Unions. In the early years there were accusations of unfairness because the quality of the recommendations for bonus awards and the moderation system was simply unable to produce an award system that was seen as fair by the majority of employees. It has now degenerated into a system that awards a basic bonus to virtually everyone just for meeting fairly standard targets. A smaller number of staff receive an enhanced bonus. Indeed the only staff who receive nothing are those subject to performance recovery action.
Average amounts received are quite modest - a few hundred pounds at most.
Anyone who thinks that the success (or not) of getting a few more helicopters into Afghanistan is down to every civil servant in the MOD is barking mad and just doesn't understand anything about how complex organisations with multifunctional departments work. Gromit hit the nail on the head. Indeed it isn't the civil servants primarily who run the supply chain operations - it's the men/women in uniform, with some civil servants working alongside.
The MOD has taken people out of its organisation over the last years, though looking at straight headcount is misleading because there is a massive amount of outsourcing going on, resulting in civil servants being TUPE'd across to work for contractors, who are taking on much of the non-core support services activities.