Duran is the only one that dies. I said I would explain it! Trust me, it makes sense!
ADDITION:
Alright, I just re-read my story, and I admit it: it completely blows. I just came up with it off the top of my head, and it's really crammed together and doesn't work well with the characters at all. I actually went out to get a sandwich, and the whole time I was thinking "What the hell was that that I just wrote?"
But it does make sense.
So, when they "rescued" Stukov from his infestation in "Ressurection," he reacted a little bit upset about it at the time, but he went with them. He also would definitely hold a grudge against Duran for trying to kill him. The idea that I had would be that Stukov hated being so powerless, so insignificant. He hated it to the point where, in the mission following the one I described, he would show up on Kerrigan's doorstep and allow himself to be reinfested, maybe even because the nanoserum didn't work entirely: the infestation could still have some small grip on the back of his mind. Thus, replacing Duran as Kerrigan's sidekick.

Another thing that would be significant about Duran dying is that now the Hybrids will be without a leader, and will lash out against everyone randomly. I thought about having them all gather over time around the temple on Shakuras (since that's where they would be drawn by the power that had been controlling Duran), and maybe even grow an entity similar to an overmind.