Not sure on this one.
She is being provided a company car, so that is treated as a "Benifit in Kind" by the tax man. Basically, they deem the supply of the car to be worth an amount equivalent to a % of the new price of the car, and it's CO2 emmissions. Usually comes out at about 15-20% of the list price of the car. So if the new car cost £15K, they would deem that the Benifit in Kind is worth 15% * £15K = £2250. HMRC treat this as if you were being paid an extra £2250 in salary per year, about £190 per month, and they tax you on it.
You normally have 2 choices with the fuel. Either the company pays for all the fuel, and you keep detailed notes on how much personal milage you do, and re-imburse the company for any personal miles. Or, you buy all the fuel, and you submit an expenses claim to the company for fuel used on company buisness. I *dont* think you can claim the 45p/mile HMRC allowance - that's for using your *own* car for buisness use, and is intended to cover the cost of depreciation, wear and tear, insurance etc.
What I think your wife should be doing is submitting an expenses claim to the company for the fuel she buys for company use. If that's difficult, keep notes of milage on company business, and divide by the MPG and multiply by the price per gallon. Then once a month submit an expenses claim, and they should re-pay her this expense - £1200 in your case. If the employer won't do this, take it up with her union. Her employer can't expect her to pay for her own fuel. This assumes that there is no "fuel allowance" element to her salary.