Where this could be cool, is if for whatever reason you have a NPC that is chaotic but is trying their best to not show it, all of sudden they become good, and I mean really good like sparkles and fairies and rainbows good. And now your Cleric or Paladin rather than being virtuous, are the embodiment of evil. Obviously this premise would take some doing/planning on the part of GM. Orcs are good, fairies are evil, dragons are good, elfs & halfing's are evil.
Within the episode the 2 sides had to work together for the common good of both worlds, as the balance of good & evil was extremely upset by having the counter parts in the wrong worlds.
Its a interesting premise, one that I may take further.