Maybe, but there is no way you can assign these to the cost of a particular leg. I am talking about pure variable-cost that are incurred by a particular flight (fuel, maintenance, landing, etc...), and not some of the problems you mentioned that cannot be quantified.
Thats sounds like something comming out of management. A management oblivious to losses.
An airline loses money by incurring more costs than making revenue. As to RASM on the outbound Bahrain flights, especialy to Europe, is pretty healthy, even in the back cabins, it would suggest that the losses are coming from base costs.
And in your own words:
Long haul from MCT: LHR, BKK, KUL, CGK (4)
GF is maintaining a base for 4 destinations?