I don't know why it was changed to this in SWTOR, perhaps the designers thought simply that red is more evil than yellow. I mean, even the Emperor himself has red eyes.
yeah i don't understand it either, i searched through the Lore and Internet but nothing about Red eyes for the sith, Malgus has the closest eyes color according to lore and sith Legends(i mean when i compare every other sith in game to Malgus)
however since it exist in game for Malgus i hope we will get the same, let say like a deed once you finish it the color of your eyes becomes more and more like a real Sith. i understand that some players think the red eyes make a cool look for their characters but in Lore its not true.