They could use how Peacemaker ended to do an adaptation of the "Dead Issue' story from the OG Suicide Squad comic where the Squad was exposed and Waller was going to lose everything so she did one last off book mission with specific members of the Suicide Squad to take out some voodoo drug kingpins who had been a pain in her ass for a while.
At the end of it the voodoo drug kingpins all got murdered, Waller deactivated the brain bombs in the Squad members who helped her and let them go, and at the end of the story Waller went to jail for all the shady shyt she had done as head of Task Force X.
Just change the voodoo drug kingpins to something less stupid and the basic concept would work: Waller feels the walls closing in on her with her daughter's revelations so she goes scorched earth to settle a score/close the book on a final mission before she ends up in cuffs.