I still haven't finished Lockdown, so maybe my current assumptions are totally wrong, but from what I've read so far, I get the impression Deus is not the main threat. He is not the mastermind behind CFD, and is, in a way, a victim of it. Project Vulcan was meant to be able to reunite a e-ghost with a body (namely, put Cerberus back into Eliohann). I suspect Dodger also had a hand in it, to put his sweetheart AI into a meatbody somehow (come to think of it, that's pretty creepy).
PAX brought back Deus to sabotage the project to her own ends and create chaos, maybe to feed her Dissonance pool. The current form of Deus is just a rabid, confused beast unleashed by PAX. I think she's really amused to see her former master reduced to this sorry state.
In other words, this second (third?) coming of Deus is just a distraction, a red herring. PAX is the true evil this time around. While everyone is busy freaking out over Deus' return, she is free to achieve... whatever she's trying to achieve.
That's how I see it so far, at least. Fortunately I'm on a business trip in a few days, plenty of time on the plane to finish the book ^^