I am no doctor, but what you are describing sounds like 'geographic tongue.' I know this because I have this. If you Google it, you can see some pictures to kelp you see if it looks like what your baby has.
There is no treatment for it and it is nothing more than an annoying and yucky looking. In my case, it gets aggravated by citrus and spicy foods. Certain toothapstes will also cause me to get the spots on my tongue. My Mom told me that when I was a baby, she took me to the doctor, with the same fears that you have.
When I eat these things, I get the smooth, red spots on my tongue. They clear up and reappear in other places. If I eat too much acid, especially ketchup, I can get lots of spots and it might hurt a bit, but I does clear up. Sometimes drinking milk or eating TUMS helps.
This may not be what you are seeing, but maybe it can help.
While I can understand your concern, the doctor said your baby was fine.
I think you would get some really good advice about this conditon over on one of the baby forums. They would probably understand about this condition, have far better advice than me AND understand your anxiety about it as well.
Please do yourself a favor and talk to the good folks over there.
Peace
Greenlydia