Poster, the church did the right thing for one reason, i.e. setting an example for all. You may be right that many might have had intercourse the previous night and gone on to the altar to be married. Truly they're not any better than your uncle's case and the only reason such marriages go ahead is that the pastor and all others trust that all is well. As you may be aware, humans have not been given the ability to know everything about everybody (i.e. omni-conscience) - which attribute belongs to God and God alone.
You may get some comfort from this: any couple intending to marry that purports to their pastor that they've not had intercourse before marriage when in fact they have will be marrying in church by false pretences (which is sin); and God will not be part of it - any blessings recited will simply be empty pronounciations. And going to another church is no solution at all!!
So if was me in that situation, I'd come out clean and repent so that when we I do get married in church, God will be in it.
So cheer up, God cannot be deceived!
My Brother, if it was you, the story would be different.
Many times, we place standards that we cannot meet.
Back to the topic. I think we place so much value in church weddings (not that it is bad), but the true marriage is in the payment of dowry (even biblically speaking). So go to her village pay her dowry, celebrate and if the church refuses to marry you, its okay. Just march to the court an get married and move on. Even God will recognise your union.