Is it permissible for an accountant who embezzled money from his former employer—who had not paid his salary and denied his rights—to give the embezzled amount as charity on his behalf, or must it be returned to him after repentance?

What you did, taking money unlawfully, is a grave sin, and you must repent and feel remorse. Returning the money was obligatory upon you. Since this person denied your right and you could not recover it through open means, it is permissible for you to take your right from him, provided that this right is established. As for what exceeds your right, you must return it to him without informing him of how you took it; rather, it is sufficient to inform him that it is his right. It is not permissible to give the money in charity on his behalf unless it is impossible to deliver it to him or to his heirs.