There are two separate issues here it seems to me:
Firstly there is whether or not anyone should be allowed to bring alcohol on a plane to Dubai. The Government of Dubai is entitled to permit this or not as it chooses (Qatar doesn't permit it for example, even though alcohol is available in Qatar). That law should apply to everyone equally, passengers and crew. However the airline is entitled to apply separate rules to its employees - when you are flying you are at work and responsible for the passengers and equipment of your employer. The airline could say that it does not want employees bringing any alcohol (or a limited amount of alcohol) on to its planes and it would be perfectly within its rights to do so - most workplaces the world over do not allow employees to bring alcohol on to the premises.
The second issue is the application of a charge/duty by airlines on alcohol brought into Dubai by airline personnel. Here the airline has no rights whatsoever. Duties are a tax levied by Governments only, and not by corporate entities. The taxes paid by airline staff resident in Dubai should be the same as those paid by any other resident of Dubai.