I always assumed that they wound up free from their mind control.
When Geperuniti went out of control and began draining spiritia from friend and foe, the Varauta army was probably drained too, leaving them in a coma with everyone else. When Basara's singing became powerful enough to awaken UN Spacy, I'm going to guess that his singing also snapped the Varauta army from their coma and mind control. We don't see any hostile activity from the Varuata immediately afterwards, so one of two things must have happened: they were freed by Basara's singing, or they remained in a comatose state. If the latter occurred, then I'm sure UN Spacy revived them on their own.
Maybe Geperuniti freed them before leaving, but seeing as how he forgot to give Ivane Gyuntar back control over her own body, he probably too fixated on the future to be bothered. They were all just pawns, after all.