I would definitely say go with what the consultant suggests since consultants (generally) are experienced and have come across all sorts of brides and occasions; if they say get your dress measured for heels if you are planning to wear heels for your reception, you probably want to do that. It makes sense to me since you'll be wearing them longer - ceremonies are usually shorter than receptions. When you walk down the aisle barefoot or with flats/flip flops, you'll just want to be a bit more careful and walk a little slower. I don't think it would be that drastically different, particularly if your heels are not more than 2.5 inches. If you think the extra fabric is going to trip you up down the aisle, maybe you want to look for some wedges. Those will have similar heights to the heels and you can walk down the aisle without your heels sinking in the sand.
I'm wearing flip flops for my ceremony and probably taking off the shoes altogether for the reception since both will be on the sand. My mother practically flipped out (ha ha) when I told her about flip flops. But then she calmed down when I showed her that they weren't those regular Old Navy type flip flops. I do have a pair of pretty heels for photos, just in case, but I doubt I'll actually put them on as I'm not sure what it would look like since my dress was hemmed for flip flops. I guess we'll see.