Silvanas eyes turns from red to blue when the two fragments of her soul are reunited, it also goes to show that her "good side" is in control now, but she is not the only one with red eyes, nathanos and the dark rangers also have their eyes red and last i checked they were not killed by frostmoune, so their souls are complete. They have red eyes because they are the special type of undead that have their body in perfect shape, but what does the red eyes mean for them now considering what happened with Silvanas??.