The "Holy" part of marriage is completely up to each church to decide for themselves without government interference.
The "civil" part of marriage is what we are talking about. As long as the government is involved then the constitution applies.
It has already been established that "separate but equal" is not constitutional. So saying that one class of people can get married, but another has to get a civil union is not equal. The 14th Amendment to the constitution demands "equal protection under the law." The only way that same sex couples can be treated equally is to grant them marriage.
It would be great if this were something that each state could decide themselves. But the US constitution will prevail if a state adopts something unconstitutional, as has happened. That's why DOMA will eventually fall. Marriage equality will eventually be granted to all.
So it is written, so it shall be.