Can you complain enough to get a new granite top?
I think you will have to raise the whole kegerator, or better yet install some sort of decorative wood to cover the hole in the granite and then install the tower directly to it. If you cannot get them to make this right.
Most installs, that I have seen, you would take the tower off of the kegerator, cut the hole in the top large enough for the beer line, and then attach the tower to the countertop. That would be my first choice.
Looks like the hole was cut large enough to take off the tower for the install.