From the bits of dialogue I remember, we don't know that Khan would have performed "missions" for Marcus. Supposedly, Khan provided input on how to build new weapons, or at least how to improve on them. This may well have been a full-time job, but more importantly, it is likely to have been a short-leash one. Marcus wouldn't have much motivation to let Khan wander outside Section 31 think tanks.
At least not until he chose to use Khan as an excuse for starting the war with the Klingons. Did he choose that after Khan rebelled and escaped? Or was the rebellion and escape part of Marcus' plan?
I think there's some tie-in material online, stating that Khan did do some field work for S31, specifically investigating Klingon activity in the Phaedus system. Perhaps Marcus felt that with the rest of Khan's people in his possession, Khan would not try to escape or overstep his bounds, out of fear for their lives.