You can only calculate a proper CI if you know the cost of fuel, the total of all other operating costs, and the factor applied in the cost index formula for the specific airplane. In general, that is readily available only in the case of a "wet lease" airplane, where the lessee pays separately for fuel and a fixed operating cost to the lessor for all other operating expenses. Over a relatively short time the average fuel burn for the route structure can be determined, so the CI offsets can be directly applied.
For most passenger airlines, schedule is more important than fuel burn, so CI is either ignored or adjusted to yield the desired speed.