The Reformist camp is ideological. It is based upon the perception that major political institutions need restructuring. It requires change in Iran's power dynamics. However, practically, it cannot succeed in a conservative dominated Majlis and with a Council of Guardians and Velayet-e-faghi that care nothing for reform, but to maintain power. Moin has to recognize this and must know that practically, even if he were to become president it would completely eliminate any backing the reformists currently have, including his ability to bring about change.
On the other hand, to step down, in complete defiance of Khamenai's charge would be a significant step that could lead to the political empowerment of Reformists. Social discontent with Khatami arose in large part because he would not take aggressive measures to defy Iran's political institutions. Khatami would not step down when urged by his constituents when, time after time, his political proposals were vetoed by the Council of Guardians.
By embracing Khamenai's decision, Moin does nothing more then implicitly accept the current political situation. Worst, it does more to collapse the distinctions between conservatives and reformists amongst the population. This is a far greater threat to the reformist parties then to be politically disenfranchised.
The success of the reformists is on maintaining and spreading their ideology, not upon securing seats in the Majlis or Presidency. Only by stepping down and not accepting his certification to run will Moin be effective in empowering his party.