I am making a wedding cake that will be covered in fondant. I've read that fondant doesn't freeze. What do you recommend if the happy couple want to save the topper for their 1st anniversary?

When you say 'topper' do you mean something you have made from fondant that goes on the top tier or do you mean the top tier itself?

What you can do is give them a certificate for a free 6" cake on their anniversary. Or instead of the certificate tell them it will be free if they call (5 days?) in advance of their anniversary.
I also have read many couples are choosing to partake of their 'anniversary' cake for their 1st month instead of waiting for the 1st yr.