I think Cumberbatch is playing a Eugenics War survivor who joined Starfleet under an assumed identity so he had the resources to track down the Botany Bay
. I think Carol Marcus and the Peter Weller character are in on it.
Hmmm...Carol Marcus being "in on it" would certainly be an interesting twist.
However, the writers would need to convince us that Carol had a valid reason for being in on it. I think if she is going to be "Carol Marcus", she still needs to be a very principled person, no matter which of the two universes she comes from. Having said that, people are certainly apt choose unconventional sides of an issue, all for the sake of Principles.