It's really hard to say what exactly is going on - and honestly, that's why the subplot appeals to me. It's showing a different side of things.
While I'm hesitant to make such a statement because I have nothing to back it up, it might be that whole tidbit was actually Unukalhai acting on his own. He admitted he was being emotional about the abuse/use of Primal power. Lahabrea's Lesser Ascians were independent as well and while they seem to follow his orders, they also acted on their own.
I'm wondering if he was even supposed to tell you what he's told you - alternative, perhaps he was, and that's part of Eli's plan. It's the whole "unpleasant truths can be hard to swallow whole" thing. Feed us them slowly, bit by bit, and they're easier to accept. I mean Elidibus is Elidibus, but even that seems rather far-reaching, even for Second Best Ascian, so I'm more willing to say he's telling you things he's not supposed to be sharing.