Wow, amazing all the fun I’ve been missing! So many points to address, so here goes.

religion has no baring on this discussion
While marriage may not be religious in nature to everyone, there is no doubt that it is VERY religious to a lot of people. Therefore religion is necessarily part of the discussion.

Marriage does not belong to the church/Atheists get married all the time/etc.
True, but you can’t fault the church for being upset when a sacred tradition of the church gets redefined as something else. It necessarily means that one group is going to lose its concept of the word. Imagine if the government started giving benefits for those who have been baptized (never mind that this is a ridiculous example, the point is that baptism is a religious “rite” on par with marriage). Then the state decides to redefine baptism to include all those who’ve ever jumped in a swimming pool. Of course the church would object, saying the government has no right to redefine the term. This is the way the church feels about marriage. The church would claim the concept goes back to Adam and Even, the very beginnings of mankind, and that it was a religious institution then. Of course, the non-Church will disagree and there’s the rub. The bottom line is that it IS going to happen, and the Church IS going to feel betrayed by it. “State” marriage and “Church” marriage should have been separate concepts long ago, but they’re not, and that’s just the way it is.

The Old Testament Commanded the Killing of Homosexuals
It did, to the Jews at least. But there are three distinct parts of the OT Law. Some laws were ceremonial, relating to the worship practices to show honor to God. Some were governmental, relating to how peace was to be kept and what was lawful or unlawful for “God’s Chosen People”. The last type of law was moral law, which directly relates to the character God expected his people to have. The first two types of law do not directly correlate to today’s world because we are no longer in the Jewish religious or political systems. We are still, however, to obey the moral aspects, which dictate our character. In addition, while the first two parts of the law are not directly applicable, there are still things they tell us about the character of God, and those “moral” aspects must still be followed.

The penalty of death levied against many different sins (not just homosexuality) was a function of the governmental law of the Jewish people so it does not translate into today’s world under a secular (or at the very least, non-Jewish) rule. However, we can still understand that God views homosexual acts as sinful.

Separation of Church and State
The first amendment was put into place to protect the rights of churches and religious organization from persecution by the state. The state was not to enforce what people should/should not believe; it was up to the individual. Many Christians today feel that the first amendment has been twisted to mean that the state should be protected from the church; the reversal of what was intended. I think the amenders had every intention of religion affecting the governing of the United States.
In either case (denying or supporting same-sex marriage) the state is not interfering with the church. Church’s have been marrying same-sex couples for quite a while, and no ruling of the state is going to change that. Likewise the state will never tell a church that it must recognize a same-sex marriage if the church doesn’t want to.