CC, a marriage break-up is a personal thing, and no matter how much anybody thinks that service life contributes to any such break-up, it really is not their fault. Your wife married you knowing you were in the services and that could mean extended time away from home etc.
You chose to live in a quarter, under quarters rules, not a private home, would you expect the MOD to pay you to move out of a private home in the same circumstances, I suspect not.
Neglible fuel costs are still fuel costs, also include any vehicle wear and tear costs, insurance etc, as I believe that service vehicles are NOT insured for private usage.
As to morale and welfare, the MOD doesn't give a stuff.
All the best for the future, I just hope you can fully get rid of her before your promotion.