** Spoilers **
Carter summed up my feelings in this episode by essentially saying stop inventing this stuff. No beta test before rolling out nano-dust? Why not test in a remote part of the desert? It would be nice if there were more episodes with different plot points, the "super-geniuses almost destroy the world" has been done to death. I still enjoy the show but I can see why it's ending - they haven't been able to come up with fresh ideas in a long time.
As for this ep, I agree it seems likely the "villains" are the control program entities from the virtual Eureka. Henry, Carter and Jo were the control programs I recall from that story so it does fit. When Carter saw the thing in the tank become him it was a nice homage to the Body Snatcher movies or at least reminded me of them.