he has accepted his resignation letter
means what? Who is he to accept his own "resignation letter"? Have you given to him any format of resignation letter? Coming to your query -
If you have concluded the disciplinary proceedings, then you have to verify with the disciplinary authority of your organization what is the quantum of punishment awarded to the employee. It can be 1. Compulsory retirement 2. Dismissal or any other form of retrenchment existing in your organization's service rule book. It the quantum of punishment is dismissal which makes the employee forego any terminal benefits, and resignation does not entail foregoing of terminal benefits of employee, you would be technically wrong in accepting the resignation letter.
If yours is a Banana Company (as in Banana republic ) without any Service regulations, Conduct rules it means there won't be any difference between removal by company / resignation by employee. If you have been submitting any statutory compliances under Industrial Employment Standing Orders Act, then be in the know about the Service regulations of your company and follow as it is said in the above (first paragraph).