Is it permissible to repay stolen money to the company by purchasing supplies for it from the same money when requested, without the owner's knowledge?

You have done well in obliging the person to return the money to his workplace. He is not obligated to inform the manager; rather, he may return the money through indirect means, such as those you mentioned, or by depositing it into the company's account without informing anyone. This is due to the Prophet, peace and blessings be upon him, saying: "Whoever has wronged his brother... let him seek forgiveness from him today," and "The hand is responsible for what it takes until it returns it."