Two sources:
1.
Wowpedia: "At some point after becoming nerubians, their society broke away and opposed the Old Gods that their people once served as aqir, specifically Yogg-Saron.[5]" This should be taken with a grain of salt, but I imagine they got their information from somewhere credible, I just haven't dug enough.
2. WoW - Ahn'kahet: The Faceless Ones quest
Seer Ixit: (Quest wants you to kill 3 Faceless Ones and Herald Volazj)
In my peoples' struggle against the forces of the undead, they dug deeper as they lost ground.
They inadvertently exposed minions of the Old Gods known only as the Faceless.
In the end, we could not fight a war on two fronts.
With your aid, perhaps the Faceless will finally fall.
-----
If they were allies to the Old Ones, specifically Yogg-Saron given its Northrend, they shouldn't have been attacked/killed by the Faceless Ones. This is speculation on my part, but it seems to make sense.