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Of cource to accept the resignation is hassle free for U, but in organisation geting rid off from such employees, its also necessary set the precedence by summary termination, for not repeatation of such type of behaviour in future.
Always choose the "lesser evil". Better to accept the resignation letter than to continue the due process of termination.
I have a similar case where an employee is on AWOL for 60 days already. Our policy provides for a penalty of termination for this case. We sent d first notice to d employee through his last known address, and we received a resignation letter as reply. Although we can push through with the penalty of termination, our lawyer recommends for acceptance of the resignation instead. In the resignation acceptance, we still indicated his act of AWOL to emphasize that this behavior is unacceptable, and confirmed his voluntary resignation from employment effective on the date he started his AWOL.
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.

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