I assume that this happened in the Philippines wherein an employee's effective date of resignation is 30 days after submitting the "letter of resignation." Therefore, the person who committed serious violation is still, technically speaking, under the employ of the company.
In this regard, the company can still serve the notice of termination before the effective date of resignation and all benefits accrued to him may be forfeited based on existing company rules and regulations.
In my opinion, the company should have not accepted the employee's resignation because there is already a sufficient ground for termination even before it (resignation) was filed. Second, it is useless to indicate AWOL (absence without official leave) when the employee's resignation was already accepted. Non-conformity or violations of company policies are best indicated in a termination letter and not in accepting a resignation.