Either wear some other shoes while riding, and change when you get to your destination, get a shifter that doesn't have the rubber on it that marks up your shoes, or get some covers for your shoes that keep them clean. You could replace the rubber shifter part with something made of silicone or other material, but it might get dirt on it, and you would spend time cleaning it....
seems like having a cover would be as much of an inconvenience as swapping motorcycle boots for shoes.
maybe get all your shoes in black? that might be an option. Wouldn't show up dirt or scuffs that way.
I assume you are talking about the marks on the top of the shoe from the shifter? Your best option is going to be 2 pairs of shoes. One while riding, another when you get to where you are going. Either buy a pair of boots that are comfy and meet your sense of style, or get another pair of boots and some luggage that will let you store the boots when you get to your destination.
Threads like this are why I hate the internet.