I think Abby cited the only two options, either comply or don't go. Actually, there is a third, switch dresses.
I don't think you can ignore the request. The couple have obviously decided that appearing taller is more important than attendance or they wouldn't have made such a crazy request.
I think it is completely wrong of a couple to require specific clothes be worn or heel height, just like I think it is crazy for a couple to believe a sunrise wedding is a great idea. But the couple of made this a condition of your attending.
Based on your relationship with the couple, you have to decide what your willing to accept.
So you either wear a different dress and flats, buy a pair of flats, or stay home.