The best way to handle this is with account-specific API keys. Even that would just mean creating an account, and the only real benefit to that is that you could track the API key, and if it did "bot-like" things, ban it. That's not really a fix, just a barrier for entry, preventing poorly thought out bots from working.
I'm pretty sure this already exists. These APIs have been in development for a couple of weeks now and as far as I can tell (from watching the /r/pokemongodev subreddit) there haven't been any bans. Niantic, at present, don't appear to have any automated system attempting to catch bot-like behavior.
