What is the correct action for an employee who illicitly took money from the price of a purchased commodity, and has repented and wishes to return the money but is financially unable to do so, and cannot return it to the same entity?

What you did by taking the money is considered usurpation of another's property and an aggression against it, as well as a betrayal of the trust that Allah has forbidden betraying, by His saying: "O you who have believed, do not betray Allah and the Messenger or betray your trusts while you know [the consequence]." This sin necessitates sincere repentance, and part of its completeness is returning the money to the party from whom it was taken; due to the hadith: "On the hand is what it took until it renders it." If you are unable to return it now, it remains a debt upon you until you are able to do so. If it is absolutely impossible to return it, then spend it on general Muslim welfare or for the poor and needy.