I think there's an even chance that she'll appear to die during the climactic battle, and then we'll get an after credits scene of her waking up in Belle Reve with Amanda Waller standing over her, gleefully telling her all about the nanotech explosives coursing through her blood as she welcomes her to the Suicide Squad.
I think Flagg is likely gone, probably so they can elevate Deadshot to the role of team leader. If they had cast Tom hardy or Jake Gyllenhaal like they tried to, his odds would be better. But Joel Kinnaman is a prime candidate to die a heroic death.