You go to war with the brain you have, not the brain you wish you had. The best you can do is be aware of these emotionally-charged valences so that you are able to discount them when appropriate.

Besides, even if you could completely turn off these processes, I am not sure that you would want to. By calling it the reptilian brain you make it sound like it is only appropriate for reptiles. The fact is, the same system that tells us instinctually that snakes are threats is probably involved in much of what is called "people skills". Normal social interactions would be at a huge disadvantage without them.