Is it permissible to combine the price difference obtained through negotiation with the seller and the legal brokerage commission, or must one of them be returned to the company? And does the company's agent incur a sin by accepting this?

If the company's agent is authorized for what was contracted upon, then the contract is valid, and it falls under permissible brokerage. Violating the law by exceeding the estimated limit in brokerage does not affect the validity of the contract or the lawfulness of the money earned from it.