If you are set on using round graham crackers, why not cut the graham crackers with a biscuit cutter. Even if it breaks into pieces, you could still place them in the cupcake papers and the filling will kind of 'glue' it all together and they would never know that it was broken. I am sure that if you were really careful that you can get them cut without much trouble.
By the way, please share your recipe, please, please, please...