The fact that one of you worked and the other didn't has no bearing on what filing status you can use.
If you were married as of December 31, 2016, you can't do anything now. You are not allowed to amend from joint to separate returns after the original due date of the return.
If you were not married as of December 31, 2016, your joint tax return is what is called an "invalid joint election" because you were not legally married at the end of 2016. This is an exception to the general rule that you cannot amend from joint to separate returns after the due date of the return. If this is your situation, you can and should amend the incorrect joint return, but a special procedure has to be followed.
This is a very uncommon situation, and it's a very obscure part of the tax rules. I recommend that you have a tax professional prepare your amended return with the attachments that the IRS requires. You probably won't find a tax pro who is familiar with this particular situation - it doesn't come up very often - but look for someone who has experience dealing with the IRS in unusual cases. You can tell the tax pro to refer to IRM 21.6.1.4.7, which is the section of the Internal Revenue Manual that covers an invalid joint election. When you meet with the tax pro, bring a copy of your original joint tax return.
To get your amended return accepted, changing the filing status from joint to single (or head of household if eligible), you have to first of all clearly state that the original return was an "invalid joint election," and explain the circumstances. Since this is such a rare situation, I would also suggest that you reference IRM 21.6.1.4.7. The tax pro will know how to word the explanation. IRS procedures require two things in order to accept the change of filing status.
1. Documents verifying that you were not married as of December 31, 2016. The Internal Revenue Manual has a list of acceptable documents.
2. An allocation of all "income, credits, and payments" on the joint return. "Allocation means the taxpayer must designate/show which wages, deductions, withholding, EITC, tax liability, etc., belong to each taxpayer." Here's where you really need a tax pro. There are very detailed rules in the Internal Revenue Manual about how to do the allocation (IRM 21.6.1.4.8).
This is not something that's covered in normal IRS instructions or publications. If you want to look at the applicable sections of the Internal Revenue Manual yourself, go to the following link, then scroll down to 21.6.1.4.7 and 21.6.1.4.8. The Internal Revenue Manual is the manual of procedures followed by IRS employees. It's written for them, not for taxpayers, so it is addressed to them and assumes a level of knowledge that they have from their training.
https://www.irs.gov/irm/part21/irm_21-006-001r.html#d0e234
