Now that I've got Tilemap Town running on a server with a gigabyte of RAM instead of 128MB, I really want to get user-provided scripting implemented. I still think the best design is having an "official" bot that runs on the same server (and thus has no latency), sits in some admin map, and remotely interacts with any map that's set up to use its services.
If I don't have some specific function for uploading code to a bot like that, it could be funny (but practical) to send a bot in-game mail.