Just to be clear on the point about Federal gov't not recognizing as married.. that should have said does not recognize "unmarried" domestic partners as married on tax return. If legally married then yes, they would file married/joint or married/separate. See article below from IRS.
https://www.irs.gov/pub/irs-utl/OC-SamesexmarriagesnowrecognizedforfederaltaxpurposesFINAL.pdf
