I personally think that is an easy solve, I pay menu prices plus tip. If the place adds something to the check regardless of what they state it to be, I consider that part of the tip. Not my fault the person works there and decides to stay, anybody that is good has a lot of options to go elsewhere. Cold as that may sound, I sleep fine and I don't know of a single place that I am not welcome back at.
It sounds easy, but is super uncomfortable. The waiter at Sublime acted so shocked that we didn't want to give additional tip for what I considered borderline food and service. We will not be visiting there again, but it was not a fun experience. Bringing more cash this time to do as Kim suggests and leave a little extra if warranted, but I personally am not looking forward to navigating servers asking for extra tips.