Whle I understand that the government cannot legislate beliefs held by any religiious organization, the separation of church and state is not meant to protect any church's ability to discriminate.

Anyone in this country can set themselves up as an ordained minister and commence to taking all the tax advantages offered by our laws, but then they do not want any laws which seek to tell them they they must act in accordance with society's accepted norms.  There was a time when churches refused to marry inter-racial couples, because they did not believe it was "natural."  Eventually, this form of discrimination ended, but it took legislation to make that happen in much of the country.

I know same gender couples who have adopted.  They are devoted to their religions, their partners, and most of all, their children.

It is important for organizations, whose mission it is to place chldren in loving homes, to carefully select the homes and what kind of parents the occupants therein will be.  These selections should be based on the parents' ability to provide a safe and stable environment, which can be done by both traditional and same gender couples alike.