How does a person purify himself from unlawfully acquired money taken from his company without its owner's knowledge, given that his entitlements exceed the amount he took?

The employee is a trustee over the company's funds, and taking from them without the owner's permission is a breach of trust and an act of betrayal. He must repent. As for the money taken, he is not required to return it if the company owner has procrastinated in paying him more than that amount. In such a case, it is permissible for him to take it secretly, provided that it is not an act of denial or procrastination on the part of a wealthy person.