How can one clear himself of liability for an excess amount received as salary, knowing that returning it to the accountant may be difficult, and is it permissible to donate it as charity?

You must repent to Allah and then contact the company owner to inform him of what happened. He may either forgive you the excess amount or take it back from you. Donating the money is not sufficient as long as its owner is known. Therefore, you must clarify the truth of the matter, for Allah Almighty says: "Indeed, Allah commands you to render trusts to whom they are due," and the Prophet, peace and blessings be upon him, said: "On the hand is what it took until it renders it back."