Well I usually stick to the films (Original Trilogy) when it comes to stuff like this. For example I just hate the purple lightning in SWTOR, when it should be blue like in ROTJ. But admittedly, red eyes are cool (despite Emperor having yellow in ROTJ).
Still if you don't like the red eyes (and black dirt around your mouth
) you can easily select yellow eyes in the character customisation (they are actually basic colour for humans btw) and disable dark side effects. I on the other hand, cannot change the stupid purple lightning.