Is the money the accountant received, as a result of the seller's deduction from the price of the goods, lawful or unlawful?

You are not permitted to take the excess amount because you are an agent for the company in the purchase. The excess must be returned unless the company authorizes you to take it. The seller writing an untrue price is deception and fraud. You must inform the company; if they permit you to take the remainder, then you may, otherwise not.