A really easy fix for this is to actually do the separation of church and state thing right! Why is it that ministers, priests, rabbis, etc... are able to perform legal marriages in the first place? Why do the religious/personal vows have to be confounded with the legal agreement to combine the households of two individuals? The government should be concerned with the contract between two people. The church should be concerned with the spiritual/religious implications of those individuals choosing to marry according to the rules set forth by their religion. The two are different things.
So, to solve the problem of who can marry whom, why not make marriage a purely religious thing. If you want to get married, make vows to love, honor, and, depending on the backwardness of the religion, obey, that is your personal business with that church. If you want to have your lands and properties legally combined in the eyes of the government, sign a contract giving you the rights a privileges that marriage imparts, such as inheritance, joint property, joint income tax filing, hospital visitation, making decisions about medical care if one of the couple is disabled, etc... Call it a Civil Union or a Domestic Partnership Contract, or whatever, but just don't call it marriage! That will satisfy the "keep marriage between a man and a woman" crowd. Marriage would be a religious term, used to indicate the acceptance by the couple of the marriage rites of that particular sect, while, according to the government, all that matters is that you have a legal domestic partnership contract. If you don't want a church wedding, you could just have a big party with your friends and a person you know and trust, like a family friend or favorite uncle or something, presenting the couple and letting them make their nonreligious vows to each other, but that would be window dressing, not part of the legal process, and so would a church wedding.
Keep the religious and legal separate! The County Clerk doesn't preach in church on Sundays, so why does a Minister sign binding legal documents combining two households under the laws of the United States of America?