Honestly thinking that they now drop somewhere between the Spanish Inquisition and Al Qaeda. I was doing the alliance storyline and I'm honestly shocked to see the attitude of several characters. From Grand Lector Enaara wanting to "Purify" prisoners to the LF Draenei during the War Campaign mission "Taking the Blood Gate" wanting to purge the horde from Azeroth.
It seems really out of place though it would give some hints to what went on Draenor after we left. But I always thought that to be an issue with nature consuming the spirit of draenor as told in the chronicle and that the events on Draenor are not what they seem.
It does seem to sell the narrative blizzard wants with the light/void being able to be used for both good and evil.