Does one fulfill their obligation by leaving work without permission, or is it sufficient for the company to benefit from the employee's name in social insurance for six months as compensation for that?

The questioner must absolve himself of what he did in terms of evading and not adhering to working hours, and leaving work without permission. Otherwise, he is obligated to return the equivalent amount of the wage. The fact that the company did not remove his name after his resignation, and benefited from that, does not negate the company's right over him. The company must explain to the responsible authority its error in not removing his name after his resignation. If the questioner knows that the company will not do that, then he must inform the responsible authority of what happened so that the necessary action can be taken against the company.