Yes. Married filing jointly will likely be the best option for you. The W-4 issue may not create a hardship since she probably listed single last year, but a change will make sure that next year you are all set. It would probably be best, for the largest refund next year, for her to put zero exemptions because the married status for withholding on a W-4 would create a lower tax withholding versus single.
The only other option for your filing status is married filing separately and this can carry a higher tax due to the limitations that apply to that status.
