Yes, she must file as Married Filing Separately (MFS) too. There is a provision for being able to use Head of Household (HoH) filing status, but you don't meet the rules (you did not live apart the entire 2nd half of the year).
You may want to prepare tax returns both ways (MFJ and MFS) to see the difference. It usually well worth the effort to try to agree to file as Married Filing Jointly (MFJ).
