Barak knew exactly what he was getting himself into when he adamantly insisted on marrying her even after everything he'd witnessed. Even after everything she'd done. He still wanted to marry her, as a means to punish her, yes. Punish her for plotting to have his head taken, a punishment that would keep her away from that lover of hers that made her do such foolish things.
He wanted to punish her so he married her, thereby stopping her from achieving her motives. Their marriage was his punishment to her, yes it was.
But also, there was that part of him that just didn't want to send her off into the arms of another man. Even though he knew she was a little lying witch, there was that little part of him that didn't just wish to punish her but just wanted to have her to himself.