Were you just using straight baking soda?
usually it's 1 part baking soda, 1 part peroxide and 2 - 4 parts water (depending upon your recipe). I doubt it was "eating your teeth" as tooth enamel is really strong, however, if you have a lot of build up, tartar or plaque the process of shedding this may "feel" like it;s eating your teeth.
The best thing to do is check with your dentist and make sure you don't have an existing weak enamel condition or some other condition that would preclude it's use.