Apparently Illythia is indeed dead now and isn't coming back for season 3.

tvline.com had a Q&A with the Executive Producer, here's part of it:

TVLINE | Wait… Ilithyia died too?
Oh, yeah. She’s dead. She is dead.

TVLINE | That was not made clear.
[That's] one thing I regret. If I could go back I would’ve possibly re-shot [her death scene], just so it was clear that she did, in fact, die. We had a couple of different cuts of it where we were tying her death directly, visually into Glaber’s death, which I think was a little clearer. Upon seeing the final product, I’m going to have to explain to people that no, she’s not passed out; she’s dead.


(Link to the full Q&A for those interested)

Warning: Contains massive spoilers if you havent watched the season finale yet.