Is it considered theft if an employee takes money from the company without the owner's knowledge, in exchange for a right that was not given to him? And what must he do for his repentance to be accepted?

Both the employee and the employer must fulfill the contract between them. The employee should perform their work to the fullest, and the employer should pay the full, undiminished wage, based on the Almighty's saying: "O you who have believed, fulfill [all] contracts," and the Prophet's (peace be upon him) saying: "Give the laborer his wages before his sweat dries." Allah has warned that He will be an adversary to anyone who hires a laborer, gets his work done, and then does not pay him his wage. It is not permissible to secretly take money from the workplace, unless you have a right that the workplace denies, and you cannot obtain it except through this method (the issue of al-Zafar).