"Yet the MOD can afford to pay their staff a £40 million bonus"
Two minor points - one, the MOD is the title of the Department which encompasses the three services and the CS. Your thing should read 'the civil service'
Secondly - its not a bonus, its the non consolidated element of the pay award, payment of which is designed to reduce the long term CS pension bill. A subtle, but very important difference. The CS didnt ask for it, dont want it, and would lose it tomorrow if they could. It exists purely as a means to save money.