Is it permissible to bargain with an unjust employer for a sum of money in exchange for silence about his injustice towards one of the deceased, knowing that the family of the wronged individual is unknown?

It is not permissible for you to remain silent about falsehood. You must advise your employer to repent from devouring wealth unlawfully by returning it to its rightful owner. If the owner has died, then to their heirs. If they are unknown or cannot be reached, then he should give it as charity on behalf of the owner, or spend it on matters beneficial to Muslims.