In order to give Equal rights to all couples regardless of Gender, while also respecting the freedom of religion, the US Government should remove itself from the institution of Marriage. Marriage should be allowed as a Religious Rite. Couples of all genders should be able to apply for and file as Civil Partnerships. The government can tax based on Civil Partnership status. The courts can pass judgments based on the filing status instead of a Religious ceremony. Benefits can be determined by the Civil Partnership as well.
Churches can marry couples based on their beliefs as a religious rite (There are churches that believe Love is Love regardless of gender)
Every US Citizen will share the same tax breaks, Medical benefits, and survivorship rights based on their Civil Partnership Status.