Well marriage is already a church/state thing. It’s clearly a religious institution (at least in many cases), but it’s also a union recognized by the state for legal purposes. With the same sex legislation, religious intuitions are feeling like the state is stepping on the church’s toes by redefining a religious term into a secular one.
I think this is the nub of the problem. It's a situation familiar to anyone in software engineering: the same routine has been doing two, not actually very similar, jobs, for years on end and separating the two becomes very difficult, as the whole thing means different things to different clients.

In this case, there's marriage as a religious rite, which is clearly the sole concern of the religions in question, just as other rites (for instance, the rites making someone a deacon/elder/whatever one's denomination calls it) affect nobody outside that religion. And then there's marriage as a mechanism of state: a recent study in the US found 1,500, that's fifteen hundred, places in state and federal law where married couples are treated differently from any other pairs of people.

Personally I see the unavailability of mechanisms of state to gay people in the same light I'd see unavailability of mechanisms of state to black people, or to women: that is, unacceptable in a modern society. And fixing the inequality would seem to require either barring that mechanism of state to straights, or opening it up to gays. That is to say, doing one of three things, depending on where the church/state boundary gets drawn: drawn on the state side, entirely ecclesiasticising marriage by striking out those 1,500 statutes, or drawn down the centre by calling the state-side thing "civil union" and then rewriting 1,500 statutes to use that as the term defining these couples, or drawn on the church side by entirely secularising marriage and offering it, as a democratic state must, equally to all. The third of those sounds like much the least paperwork and any religions that were bothered by that could always talk about "Christian Marriage" or even, if they wanted, "True Marriage", so long as those phrases occurred in no statute book and barred entry to no mechanism of state.

So where did this icky entanglement of religious and state goals come from? I was at an Anglican wedding recently, where the guy giving the address, who was clearly a very pious, thoughtful, and caring person, said the usual things to the congregation about Christian marriage being all about commitment, affection, and support, but then rather gave the lie to that by saying that it was also about "a man and a woman, as God intended". Oh right, gays aren't capable of commitment, affection, or supportiveness then, vic, is that what you're saying? If they are, and if those things are what Christian marriage is about, then why debar them from it?

Some years ago I was at a Southern Baptist wedding, and the celebrant was also clearly very religious, in a different way. He was also much more overt about what he thought Christian marriage was about. "Christian marriage is all about children -- about Christian families. Children are the arrows we shoot into the future(*), and I hope this young couple shoot many fine arrows in their married life." Here at last is something gays are less good at: reproducing. (Yes, there are gay foster parents, and there are lesbian couples with children fathered by someone not a life-partner of either woman. But still a much greater proportion of straight couples than gay couples have children, if only because gay couples never find themselves in that situation by accident.)

Christian marriage is a population thing, just like opposition to birth control is a population thing. It's all about increasing the ranks of the Army of God as compared to armies of other gods, or of godlessness. And anyone who thinks such base considerations, such slavishness to the evolutionary imperative, dropped off human religious radar millennia ago, should go and look at what happens in Northern Ireland when predictors of population trends produce studies showing the Catholic/Protestant ratio moving closer to 50/50: uproar breaks out.

So it's no wonder that, through most of history, states have liked marriage too -- they're just as keen on increasing the ranks of their armies as any religion. If there had ever been a state that didn't, demographics would have seen them off in the course of a few generations as their neighbours outpopulated and outfought them, or even as natural disasters or predation wiped them out more thoroughly than more populous states nearby.

On an arguably overpopulated, but certainly fairly sufficiently-populated, world, such considerations needn't any longer be informing state policy. And the effectiveness of those measures towards the goal of population growth is itself based on a rather strange premise: that of the "floating voter", the person whose sexual inclination is affected by mechanisms of state incentivising him or her one way or the other. Even if such people exist, the goal of enhancing population growth by resolving them onto the straight side of the fence hardly seems worth the cost in marginalisation of large numbers of committed, affectionate, stable -- married in all but name -- gay couples.

Peter

(*) A line by the rather pagan Kahlil Gibran, of course, and IMO unusually sexually suggestive for such a time and place, but I guess if it sounds Biblical that's good enough.