I doubt it.Bloom's fuel cells would still be cheaper to operate than a diesel generator.
If a diesel generator were used, it would be used solely as backup to grid power. Which means, those diesel generators would only be operating very, very rarely. In this case, fuel costs are not a big economic cost.
The major savings of diesel backup generators over fuel cells therefore would be in the lower capital costs for the equipment.
So far as I know, Bloom Energy does not publish precise prices for their equipment, but I'm inclined to think that a bleeding edge technology like this would always be more expensive to purchase and install than an older proven technology such as a diesel backup.
If fuels cells cannot provide electricity at a total cost (including fuel and capital equipment) less than the very cheap rates available to large businesses in North Carolina ($0.05 - $0.07 per kWh), then I'm inclined to believe that a combination of grid power with diesel backup would be cheaper.
But Apple hasn't made their costs for this equipment available to shareholders at this point, so it's hard to tell.