By default, your client will need to file MFS.  He may, however, elect to file jointly even if the spouse was a nonresident alien for all or part of the year but these are once-in-a-lifetime type of elections.

If the Filipino spouse had compensation that could be fully or mostly excluded under foreign earned income exclusion, does not have foreign business interests, and does not have or is not anticipated to have a substantial amount of net worth, it would generally make sense to elect joint filing.