I'm not sure I understand your issue. Birth parents are the link for Genealogy. However, The family relationship that raises the child IS important too and needs to be documented.
Same Sex Marriage is just the relationship, should be handled much the same as adoption or out of wedlock situations.
If the father and the mother of a child are known they should be listed. Same goes for artifical insemination and surrogate mother situations. Who contributed the "genes" should be documented, but the family should be as well.