I hope they will keep it in the game as it fits with all the other non canon stuff they put in to the game.
Actually it makes some of the non canon stuff look like canon stuff. How many Federation ships have you seen using green disruptors? Easily fixed with a color change of them so they look like phasers.
Still it is unfair in PvP. Lets say you are attempting to stack disrupter resistance before you enter combat because you see all the Klingons using green beams, but they all actually used the command to make their phasers look green... that is an exploit in my opinion.