Their fate might not have been all that different from that of the exposed and convicted Chekov. Ashes of Eden was about post-Starfleet heroes anyway, and a story like that could easily have accommodated a traitorous Chekov in a redeeming role.
I suppose it's possible. It depends on the length of the prison sentence the agent aboard the Enterprise
would receive. Valeris was likely to spend a long time incarcerated for her role in Gorkon's assassination. I see no reason why an alt-Chekov would not have as well.