Please stay with me on this. Sorry for its length.
In "Space Seed", Spock finds out that 80 or 90 of the supermen from the Eugenics Wars are not accounted for. Kirk says there's no record of that in the history books. Spock says, "Would you reveal to war-weary populations that some eighty Napoleons might still be alive?"
Hmm.
In light of what Nero did, the population of the Federation is probably very weary and probably wouldn't cope well with news of another big threat. That is, 80 Napoleons running around at a time with a weakened Starfleet and diminished Federation.
Say the crew of the Botany Bay was found shortly after the events of ST09 and transfered to a spot in London where they're being secretly kept in stasis until it's decided what should be done with them.
Cumberbatch really is simply a 23rd century human in Starfleet named, John Harrison. He becomes "the Marla" in this story. Assigned to maintain the crew in stasis, over time he becomes fascinated by Khan and what he stood for. He finds out all he can about Khan and his times, about Eugenics, and becomes intrigued by what the leaders of that time were trying to do, thinking it was not all bad, and may have actually been for a greater good (like being able to cure a dying child in 2258).
His "coming over" to that way of thinking may not be too far-fetched. In "Space Seed" even Kirk, Scotty, and McCoy showed admiration for Khan based on what they knew of him, and said he was the least violent and "best" of the tyrants (all to Spock's shock). Someone even more drawn to him may go a step further and ally with him in principle.
Harrison begins to surreptiously extract their genetic secrets and builds himself up in private like an athlete does with PEDs. Over a period of months he becomes a superman, himself. Something he hides, just as Dr. Bashir did decades later.
When a decision comes down about how to handle the crew of the Botany Bay, he's against it but is in no position to protest. Starfleet decides it would be too dangerous at this time to thaw the crew.
Harrison wanted the discovery of the crew made public, and he wants them taken out of stasis. As he sees it, they offer things to mankind that it can't get, otherwise. He feels what they felt. He is what they are. He is improved, and now Starfleet stands in the way of improving mankind. Leaving them in stasis is cruel and even foolish, so Cumberbatch essentially "outs" himself and goes rogue for their cause.
"You think you are safe? It is an illusion." That is, Starfleet knows that you're really not safe. They're scared of 80 Napoleons, and they are hiding it from you. Now, Harrison will show it. He will provide an environment for real leadership and advancement.
That would at least be his backstory. Little of that would have to shown be on screen. It could come out in dribs and drabs of exposition.
