CthulhuKefka, first off, having an attraction to someone is not a choice. Acting on that attraction is what is a choice. Unless you get raped, you make a choice about who you have sex with.
Second, you're absolutely right: The government should not be involved in telling churches who they can and cannot marry. And there are prominent churches like the Episcopalians which are A-OK with homosexuality. They have gay marriage ceremonies in their churches, and I'm not particularly aware of anyone (who is not in the Anglican community) having tried to stop them. (Or rather, not all Episcopalian churches agree on this, and they're having a sort of internal crisis now, with some individual churches deciding to go through the anti-homosexual African branch of the church instead of through the pro-homosexual US branch. But this is beside the point in this thread.)
Your statement is kind of confusing the issue, unless it's just reaffirming what we already said. The government should not get involved in what churches call marriage within their own church. If they don't want homosexual marriages performed in their buildings, no one (from outside their organization) should force them to allow them. If they want homosexual marriages performed in their buildings, no one (from outside their organization) should force them to stop.
Nevertheless, homosexual marriage being accepted in these churches is a relatively quite recent development and does not represent the opinion of anywhere close to the majority of religious communities.
The real question here is not what churches should or can do within their own organizations but what the government should do. In the last decade, almost every state in the U.S. has passed a law defining marriage as between a man and a woman. A large majority of them have also enacted constitutional amendments saying the same thing. Most people in the country believe that the government should not recognize as marriage the relationship of a same-sex couple.
The question of whether the founding fathers were Christian: Eh, there are a lot of contradictory sources. Most people writing about this issue that I've found are pushing one agenda or another.
Here's one that seems more balanced. It seems clear to me that according to the quotes that can actually be verified, the founding fathers who are identified as Deists did not believe in a God who created the universe and then went away—they believed that the hand of Providence took an active role in certain events of the day and that they were ultimately answerable to God. The Deists did not trust the creeds of the organized religions, and some of them did not believe in the divinity of Christ, but they believed in the rightness of Christian principles (principles, not "doctrines"). Even Jefferson thought Christ's teachings (the ones he thought were recorded correctly in the Bible) were good stuff. Yet they were very much against persecution of anyone for religious reasons, and were against using religion to promote tyranny. So am I.
But trotting out the names of the deists also sidelines the large percentage of the founding fathers (members of the constitutional convention, etc.) who were explicitly Christian.
Here's a link (note that while it lists all the convention delegates' religious affiliations, that doesn't necessarily mean they were practicing Christians, but it gives examples of ones who were and ones who at least were not clockmaker-Deists).
...This whole discussion also though is kind of beside the point. I'm not sure what you were trying to say in regards to whether a definition of marriage should be part of the constitution.