They should deactivate it. Weapons should remain whatever color they are supposed to be for the sake of convention. If I see green, I want to know its a disruptor etc.
I can almost garantee it will be deactivated. It doesn't stay within the confines of the cannon and that has been stated as a restriction to this game's development. I think it was just overlooked based on the plethora of server issues plaguing this game during head-start and somebody forgot to shut it off.
If they remove it I think it is silly. Because it's not going against canon any more then all the different type of uniforms and different colors available for them, ship colors and modifications, custom species never seen on Star Trek etc.
Decide if the game should follow canon or not. Federation ships should use phasors not disruptors. This color change command can at least make it look like they are phasers.