The only thing that comes to mind is heat-resistant paint for the stove and stovepipe. Following are several suppliers: #1 #2 #3. Unfortunately color choice is often limited, though white and almond are most often available.

There are two choices... Move the stove, or move the opening in the roof. Probably easier and cheaper to move the stove, and that choice appeals also because the room layout will be more functional with the stove below the opening and the TV in the corner. Plus, perfect excuse to replace the stove itself with something more energy efficient if budget allows.

If there just isn't the budget to fix it right, well... Start a savings account. In the mean time the stove pipe can be ceramic coated. More expensive than paint, and you won't have the use of the stove while you send the flue pipe out for coating, but there are many more color options and the coatings are good from 750deg. F. to 2000deg. F. depending on the particular coating selected. Look at www.jet-hot.com for colors, etc.

I think its quirky but cute. Just enjoy it. It would probably be an expensive fix.