Well, I guess firstly, the church is but one actor in the argument. There are hundreds of churches, dozens of religions with their own definitions and practices of marriage. That would undoubtedly complicate things, and would be highly unfair if we arbitrarily assign marriage as a spiritual matter under a single church, or even a single religion in the unlikely event the churches even put aside all their differences.
Another issue that springs to mind would be cultures/people that have marriage practices that aren't religious in nature, such as the Chinese. Much of the marriage process, customs and traditions are secular in nature, and rooted in Confucian notions of filial piety, the importance of the family, etc. Narrowly defining marriage in one sense is to ignore a vast cultural diversity, and ultimately, to "discredit" the marriage practice of others. It would also be prudent to point out here that the church does not "own" the concept of marriage, not the least because marriages have occurred for thousands of years before the church (or any major religion today for that matter).
I feel that many of the examples and questions you pointed out in the flow of reasoning are red herrings. For one, marriage laws have always been in a flux, and changing them would not have any tangible legal effect on marriages of previous generations. Marriages being retroactively nullified isn't the main issue at hand, because it would very likely not happen, nor should the past hold us back. Imagine what would have happened if we stuck with old execution laws because repealing them would mean that executed criminals in the past were executed wrongly?
Another point I would like to raise is that marriage, or rather the freedom to marry is a right, but just like most rights, one should not be forced to use such a privilege. Whether you find the right person who agrees to be with you is not part of the equation. The government only provides and safeguards our ability to marry and enter a union. To use another example, I have the right to vote, but I can choose not to use it.
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This probably leads me to my understanding of marriage which to some would be exceedingly simple. To me, marriage is just formally cementing a union between two people of consenting age who love each other, regardless of their gender, social status, race, religion, etc. That's just it. If a proper marriage, wedding ceremony and registration are found to be frivolously unnecessary between two people who are perfectly contented to spend the rest of their lives together, that would go down with me just as well.
My point is, people should be able to live with whomever they love, with the usual restrictions (Age, mental health and choice, etc). If they settle on marriage, go for it!
I realise that I haven't exactly answered the point of your question amid my rambling. It's a little tricky because different countries recognise the validity of marriages differently. The UK for one, has done away with common law marriages that are still available in some US states. Some Pennsylvanian counties still have Quaker marriages. Most European nations have a mandatory civil marriage.
I think the last is the least painful and cleanest of the lot. Everyone has to obtain a civil marriage, and then they can opt for a religious one. The government does not claim to have jurisdiction over the spiritual aspect of a wedding, and religious organisations can retain some of their traditional power. That could help resolve the problem of same-sex marriages somewhat, by removing part of the religious question; Though that particular headache still rears its head when a same-sex couple want a religious marriage as well. It's something I'm still mulling over.