Is it permissible for a user who used his sister's company phone line without her knowledge, and caused the company to pay his bill, to give the bill's amount as charity with the intention of benefitting the company owner, or to pay the amount to his sister with the intention of benefitting the company owner, or to pay the amount in installments, given that his sister has outstanding financial dues that the company has not paid her?

Among the conditions for the validity of repentance is returning the right to its owner if the sin is related to a human right. The money must be returned immediately if possible, and it is not permissible to give it as charity on his behalf as long as it is possible to deliver it to him. If you are certain that your sister has a right with the man, it is permissible for you to help her take it and hand the money over to her, while informing her that this is her right to avoid her claiming it again.