I don't now about a way to do so trough skins, but i dont know much about skinning.
Reputation is not accessible to plugins trough API, however they can track it manually by tracking chatlines. For example i know TitanBar does so, and also hides completed reputations from the quick overview window.
There is also AltHolic plugin that can track reputation, but im not familiar with capabilities of that one.
Both of these probably dont have the color changing capability at the moment, however it is definitely possible to do.