If you are both living here , and if she does not have a US passport yet then don't file jointly .
If you are seeking her US passport then you are in shady territory, that being said , are you out of the US for 6 or more months at the time ?
if so then you will be exempt for Federal tax payment anyway so while is a bot more paperwork if you are seeking her US passport it will make it easier in the long run .
If you have property in the US then it depends on the state on which the property is registered for tax purpose but the same as above applies how important is the US passport . That will be the major consequence in the long run.