Cancelling senior officers rights to first class travel is insignificant when set against the fact that all civil servants, not just MOD, at grade C2 and higher have the right to first class travel.
Stop the military and you immediately have inequality and possible oddities of the CS travelling in a different carriage from his military counter part.
Stop CS first class travel and you have the trades unions at your throat.
I've got it and I want it, but I have only used it twice in 3 years.