What is the ruling on a man marrying a woman when he knows her father is alive, but he sought permission to marry her from her stepfather and obtained his approval instead of her father's?

It is not permissible for your stepfather to solemnize the marriage contract of your sister due to the presence of her father. She must renew the contract in the presence of her guardian, the father, to rectify the void marriage. You must strive to reconcile her with her father and inform her of the obligation to honor her father and to beware of disobedience.