Both of you can be right
1.) they never said all conduits died, zeke said "of the thousands that died, millions were saved." He didnt say all conduits died. There is no official statement to conclude that.
2.) in the evil ending, scientist could have developed a cure for the pluage, as well as a way to make conduits human(like in x-men). They could have used this against cole and developed the D.U.P as a threat to any remaining conduits(once your human, you're human, you're vulnerable).
3.)again, scientist could have experimented with the conduit gene to create their own superhumans(like the indian guy from heroes)
SPP probably wont talk about the endings anyway