Why they just don't operate as Air France is a mystery, as it's daft having Scot Airways in CityJet colours flying on Air France flights.
This is since they are trying to keep Cityjet as a seperate airline from Air France. This is for a number of reasons. Firstly Irish labour laws are a lot more flexible than French ones, which limit workers to a 35 hour week.
Also Irish Corporation Tax (12.5%) is significantly lower than French Corporation tax (33%). They don't want to market the airline as Air France since the French tax authorities could bring a case against them stating that Cityjet is just a facade to avoiding paying French corporation tax. Also as far as I know Cityjet isn't unionised (please correct me if I'm wrong). If they integrated it into Air France presumably the Air France unions would want to be able to represent the cityjet workers.
Overall they want to keep Cityjet seperate from the rest of Air France, hence the different colours. As far as I know Scot Airways isn't actually owned by Cityjet or Air France so presumably thats why they have a seperate livery.