Is an employee's taking of his agreed-upon financial dues from the employer, without the employer's knowledge, considered theft? And what must he do if he is unable to return the amount taken?

If your employer contracted with you for a known wage and did not pay it in full, demand it from him. If he refuses, pursue legitimate channels, such as legal action. If you have done your utmost and are unable to obtain your right, then it is permissible for you to take from his money the equivalent of your right, without exceeding it, provided that you are certain no greater harm will result.