He has some idea of what Khan might do to Marcus when they get to the bridge. He still hasn't decided what he's going to do about that, either--and right now making sure the Enterprise is safe is more important than whatever ethical dilemma Marcus's death will cause.

The bridge closes in on them, though, and he has to admit that he has no leash on Khan at all.

"On three," he whispers, hoping Khan will at least obey that much.