I can't recall a wedding that I have shot where flash has been allowed inside. I think the closest was in the porch looking out when it was pouring with rain.
But do make sure you see the vicar/priest/etc about a month beforehand and also a couple of days in advance so that you can plan your attack. Even this occasionally fails, I once had a vicar give me carte blanche to shoot the wedding (he understood where I was coming from), but during the ceremony the organist out of the side of his mouth was 'much less than helpful'. Trouble is half way through the ceremony, there is no way you can pull rank on him or have a blazing row about access.
I just had to explain it to the couple and the vicar later who couldn't understand why I didn't move across as planned to get the shot.
Vicar said he would 'sort the organist out later'