I'd never recommend this as an 'every time' thing, but I've had very good luck when I tell the couple to just reenact everything critical. Face it, church officials can be brick walls when it comes the the photographers. I've been told flat out that I'm not to be seen or heard during the ceremony whatsoever. So I just tell the couple that after they recess, I'll need them to immediately turn right behind the last pew, and come right back to the altar. From there... "Ok, let's see that ring exchange again, let's get a shot of you two lighting the unity candle, go ahead and kiss the bride one more time, etc." And with the ceremony being done and over with, turn your flash back on and fire away. And you can stand wherever you want this time.
Again, I stress that this is a Plan B tactic only, but on the occasions I've employed it, everyone seemed to be pretty happy with it. The ceremony official now likes you for your brilliant consideration for his ceremony and the couple is happy to avoid the involuntary receiving line. Proceed to breathe onto your fingernails and buff them on your shirt shoulder.
"Yes, I'm gonna take your picture. You didn't think there'd be a photographer at this wedding?"