From what I understood, Peter being taken from the alternate universe to replace the dead one was one of the things that had to be "corrected", but then somehow a deal was made and Peter was allowed to live. And somehow the Cerveris Observer is the one implicated in that. I'm not sure we know much more about this.

In the human bombs episode, the crazy army general was convinced that the couriers were evil, and was blowing them up, but from what we saw, all the couriers were doing was bringing photos of Walter to the Observer. So one possibility could be that the army guy was just crazy and misinterpreted their intentions. Of course given that we don't know their intentions...

At the end, I thought it could also have been Olivia's niece they were talking about. I mean they just said "her". Dum dum dum!