The fairest thing the federal government could do would be to pass a law allowing gay and lesbian couples to form unions that give them the same rights and responsibilities as heterosexual married couples. This would give them equal rights in every state.
The term "marriage" need not be used at all, so there would be a separation of church and state. What would be involved would simply be a certification that the two partners plan to live together as a couple. Some good legal minds would be necessary to ascertain the division of money, property, etc., in case of divorce.