She doesn't have a greencard yet at all

Did you petition your wife? If so, that is all the more reason you should file together because the officer at her interview will ask why you did not file jointly.

I disagree with this answer. The law does not require a married couple to file a joint return. It is perfectly acceptable to file separate returns with the IRS so long as one indicates on the return that they are married, but filing separate returns (by checking the appropriate box on IRS Form 1040 and completing the required information). In many instances tax liability can be decreased by filing separate returns. USCIS is more concerned with seeing that married couples held themselves out to the IRS as married then they are with whether the return was filed jointly or separately.