The only thing that doesn't add up is the fact that Kerrigan (presume to be her) is intact. If Raynor nuked Kerrigan and her brood, he'd be holding a pile of ashes instead of her body which appears to be in a state of deinfestation.
While this theory sounds very plausible, I believe there's more to it then just that. Perhaps that scientist chick you need to save early on is on the helm of discovering some way to neutralize the Zerg on a biological level and has tested this on Kerrigan. And while it may end up working on her...they'll also need to use it on Tychus, the new infested prodigy of the Zerg. Remember this image?
In the first trailer video it actually displays a warning about an anomaly being detected. Does that mean he's being infested or an agent like Duran was working under cover for his own dire motives?
Regardless, discovering the truth behind both Tychus and Duran are what I'm looking forward to most in the campaign. Hopefully we get some shred of enlightenment in this game and don't have to wait until the expansions for further insight into their origins.