Q:Wouldn't the other statement part be "how can we make sure the Doctor ends up deeply emotionally scarred by his adventures?"
That is entirely true. However, the Doctor has hundreds of years of emotional scarring that he has dealt with over his life and we see the ramifications of that repeatedly. Amy’s adventures, on the other hand, comes dangerously close to Emotional Torture Porn. Most of the time, it happens because the Doctor refused to tell her something that would’ve been vital to her. Then, when everything is all said and done, she essentially gets an emotional rinse and repeat. I understand the necessity and desire of putting your main character through the ringer, but not if there’s no growth or point to it.