Its true that electrons (which are negatively charged) flow from the negative terminal of a battery to the positive, as opposed to what is called "conventional current" which flows from positive to negative. The good news is that it makes no difference to the circuit whether you imagine there is something flowing from positive to negative, or the other way round. And it also makes no difference whether you ground the positive or the negative terminal. For example most cars have a negative ground connection so that the whole body of the car is negative compared to the positive terminal of the car's battery. But some trucks are the other way round and have a positive grounded body. It is mostly just tradition that says the ground should be negative.
There are a few situations in which there is 'electrochemistry' going on, such as in underground pipes, where it does matter whether the object is charged negative or positive compared to the earth, but in a basic electric circuit it makes no difference.