Marriage is a religious institution that has existed for thousands of years - before the existence of the US government, before the drafting of the constitution, before european settlers even arrived in the US. To legislate a new definition of marriage destroys the concept of the separation of church and state.
Marriage is a social institution that has existed for thousands of years - before the existence of Christianity.
When the Supreme Court banned laws prohibiting inter-racial marriage in 1968, were they violating the separation of church and state?