Well...she "can". NC allows it for married couples who are residents of different states.
1) To do so, y'all would have to create a separate tax file (If using the "Online" software, that means an entirely new account). In that new file, she would to prepare the Federal section as MFS, and then do the NC-MFS section....then pay for the software if needed....The MFS Federal part MUST NOT be filed....then print and MAIL-IN the NC-MFS tax return. (you can't e-file NC MFS since the Federal part is not e-filed).
Your Federal tax file in the other account could then be e-filed MFJ without any state attached. (I'd recommend doing that first...unless you do my recommended #2, below)
or...what I recommend instead..
2) NC also allows you to file MFJ...but with different states of residence, the NC-MFJ Q&A would allow you to indicate what sub-part of total Federal income was NC-taxable income. This takes out the income assigned to the non-NC resident. IT also allows you to prepare just one tax file and to e-file both the Federal and NC state parts. You do need to make sure that you indicate the proper/different states of residence for each of you when you enter your names in the My Info section. Example: You might be HOR/Resident state as TX, and she is NC. That is needed such that the proper Q&A shows up in the NC state section, so you can indicate just her portion of yearly income as being NC-taxable.
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
