I am a Wedding Photographer, and also got married at WDW.....
I would say do not panic. If it were me taking the pics, I would do everything possible to keep the crane out of the shot. If totally unavoidable, elements like this can be erased!
I actually had to remove a crane from our 2006 holiday pics as there was a big re-paint of the castle in progress. A bit of Photoshop talent and you will be fine.
The whole WDW Wedding experience is so amazing that you wont even notice it and of course, if you are tying the knot at the Wedding Pavilion, you wont be able to seee it in any detail anyway.
Please feel free to PM me if you want to know anything else.
Have a great time.
Russ