In the beginning ... (dun dun daaaahhh ...) religious institutions used to control marriage.
Eventually, because it became a matter of public policy, governments became involved. For many many years, religious marriage and civil marriage were conflated; very few people now think of the two as separate. But they are. You can have a marriage ceremony in a church if you want, but you still need to submit your marriage certificate to a governmental institution, or it's not valid in court.
1) As a function of government, monogamous civil marriage cannot be denied to gay men and women. It's discrimination to withhold civil rights from some citizens on the basis of their sexual orientation.
2) As a function of a religious institution, the acceptance of religious marriage of gay men and women cannot be dictated to any church by government (at least here in the U.S. - elsewhere, your results may vary). Your church is free to discriminate in the bestowal of its sacraments and rites.
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Calling civil marriage between gay people "civil unions" hasn't worked so far because, in practice, it has not been the functional equivalent of current civil marriage. [I think this is the essence of the Iowa court decision].
Religious people can agitate to impose their values on the rest of us, but the groups that do this are morally and ethically wrong. As a member of a religion, you don't have to like gay marriages, and your church doesn't have to perform them; you just can't stop the government from granting civil marriage. Really, as a member of a religion, you are free to believe any silly thing you want without retribution or penalty from _government_, but that does not protect you from being laughed at or judged by _other people_. While you are busy believing what you want please note that gravity still works, natural selection still happens, and there are no saviors from space to take us away before the rapture.
(By the way: There are a plenty of religious groups that agree that bans on gay marriage are morally and ethically wrong.)
There were American churches that defended slavery and Jim Crow laws. They were wrong too.