Well, I'll assume either nobody knows anything or this just doesn't exist... My solution was that I ended up setting a radius that excluded the Pokestop at the end of the pier. Since the other stops are mostly within the park, the bot never leaves the grassy park area when running between the stops.
My suggestion stands that being able to fence areas to contain the bot or prevent it from going into areas you don't want or the ability to "blacklist" specific Pokestops/Gyms would add a lot to the bot. Even the ability to just set a continuous line path for the bot to follow. For example, during lunch and on my way home from work I drive a circle through the park/business plaza and it would be nice to set up a path in the bot that mimics the path I take in real life. You know, making the bot look more real...