What is the ruling of Islamic law regarding an employee recovering his right from an employer who wronged him, by secretly taking what he believes he is entitled to, given that he does not possess official proof and a dispute arose between them leading to a deduction from his money?

If one thousand riyals were taken from you without a legitimate right, and you are unable to reclaim your right except covertly, then the preponderant opinion among scholars is that what you did is permissible. This is known as the issue of az-zafar (reclaiming one's right by force or stealth).

This is supported by Allah's saying: "Except for those who believe and do righteous deeds and remember Allah much and [are those who] triumph after they have been wronged. And soon will the wrongdoers know to what [kind of] return they will be returned." (Surat Ash-Shu'ara, 26:227).

It is also supported by the hadith of Hind bint Utbah, who said to the Prophet, peace and blessings be upon him: "Indeed, Abu Sufyan is a stingy man, and he does not give me enough for me and my children except what I take from him without his knowledge." He replied: "Take what suffices you and your children in a reasonable manner."

Furthermore, it is supported by the hadith of Uqbah ibn Amir, in which the Prophet, peace and blessings be upon him, said: "If you stop with a people and they command for you what is appropriate for a guest, then accept it. If they do not do so, then take from them the right of the guest which is due to them."