Perhaps it was: "Link...I'm pregnant. And the father is Groose." And Link would be mad, push Zelda down to the surface, and shout: "How do you like to be pushed off of something?!" and then Impa would find her seconds before Ghirahim, and Link would have to go down and apologize, but must battle Ghirahim. So...I don't think it would have made any difference to the story.
I have to go with everyone else and definitely agree that it was something romantic and along the lines of "I love you". They did seem pretty close on top of the Statue of the Goddess and during the loftwing scene the romance theme was playing. So definitely think it was intended for the two! And besides, the ending really did suggest that the two had to have more of a friendship because I don't remember anyone else staying on the surface!
Some possibilities for what I half/really expected Zelda to say:
-"Link, I'm pregant and the baby is Groose's."
-"Link, I love you."
-"Link, do you see that black tornado?"
-"Link, I'm really a brunette under this wig.."
Only one is the "really expected", the rest were just on my mind when I read the thread.