Come traitors have the ability to throw a certain level cargo overboard at no cost or at a lower cost. Since the ability is always able to be activated, should a player be allowed to still toss cargo overboard based on that ability even though their color might not have been rolled?

I don't believe so, since nowhere in the rules is there mentioned the ability to throw cargo if you don't match the color. That's why you are taking a chance picking your character. I've been hosed by this more often than I would like.